I reproduced this again.
Again, fresh helm installation, and there is alpha log:
00000000000011656261792e6c697374696e672e6e616d65020a20636f: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a20636f0000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 32 99 111]
W0528 10:04:05.271085 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000011656261792e6c697374696e672e6e616d65020a323031: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a3230310000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 50 48 49]
W0528 10:04:05.393619 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000016656261792e6c697374696e672e6861735f696d6167650400000000000c49f0: could not read list part with key 0400000000000000000016656261792e6c697374696e672e6861735f696d6167650400000000000c49f00000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 22 101 98 97 121 46 108 105 115 116 105 110 103 46 104 97 115 95 105 109 97 103 101 4 0 0 0 0 0 12 73 240]
W0528 10:04:06.166370 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000011656261792e6c697374696e672e6e616d65020a204e45: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a204e450000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 32 78 69]
W0528 10:04:07.019532 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000015656261792e6c697374696e672e6c6f636174696f6e020a204361: could not read list part with key 0400000000000000000015656261792e6c697374696e672e6c6f636174696f6e020a2043610000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 21 101 98 97 121 46 108 105 115 116 105 110 103 46 108 111 99 97 116 105 111 110 2 10 32 67 97]
I0528 10:04:09.623414 21 log.go:34] Block cache metrics: hit: 479279888 miss: 4433230323 keys-added: 210222525 keys-updated: 2219115 keys-evicted: 210107693 cost-added: 3880628428961 cost-evicted: 3879930501081 sets-dropped: 462953 sets-rejected: 7334269 gets-dropped: 11802368 gets-kept: 4720027264 gets-total: 4912510211 hit-ratio: 0.10
W0528 10:04:10.846704 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000015656261792e6c697374696e672e6c6f636174696f6e02016765726d616e79: could not read list part with key 0400000000000000000015656261792e6c697374696e672e6c6f636174696f6e02016765726d616e790000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 21 101 98 97 121 46 108 105 115 116 105 110 103 46 108 111 99 97 116 105 111 110 2 1 103 101 114 109 97 110 121]
W0528 10:04:11.445106 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000016656261792e6c697374696e672e6861735f696d61676504000000000028f8ef: could not read list part with key 0400000000000000000016656261792e6c697374696e672e6861735f696d61676504000000000028f8ef0000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 22 101 98 97 121 46 108 105 115 116 105 110 103 46 104 97 115 95 105 109 97 103 101 4 0 0 0 0 0 40 248 239]
W0528 10:04:11.982254 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000011656261792e6c697374696e672e6e616d65020a33343b: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a33343b0000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 51 52 59]
W0528 10:04:12.122931 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000011656261792e6c697374696e672e6e616d65020a6f7665: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a6f76650000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 111 118 101]
W0528 10:04:12.841819 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000011656261792e6c697374696e672e6e616d65020a303334: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a3033340000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 48 51 52]
W0528 10:04:14.334646 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 0000000000000000000011656261792e6c697374696e672e6e616d65020a207669: could not read list part with key 0400000000000000000011656261792e6c697374696e672e6e616d65020a2076690000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 32 118 105]
W0528 10:04:17.034648 21 log.go:36] [Compactor: 2] LOG Compact FAILED with error: sync p/MANIFEST: file already closed: {span:0xc0057fcc00 compactorId:2 t:{baseLevel:2 targetSz:[0 10485760 10485760 16910574 169105742 1691057427 16910574274] fileSz:[67108864 2097152 2097152 4194304 8388608 16777216 33554432]} p:{level:4 score:1.4644237509096527 adjusted:2.312061263167869 dropPrefixes:[] t:{baseLevel:2 targetSz:[0 10485760 10485760 16910574 169105742 1691057427 16910574274] fileSz:[67108864 2097152 2097152 4194304 8388608 16777216 33554432]}} thisLevel:0xc00042c3c0 nextLevel:0xc00042c420 top:[0xc03e179d40] bot:[0xc0115c1d40 0xc013279200 0xc0446a9800] thisRange:{left:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 84 72 83 0 0 0 0 0 0 0 0] right:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 110 32 255 255 255 255 255 255 255 255] inf:false size:0} nextRange:{left:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 83 107 121 0 0 0 0 0 0 0 0] right:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 118 97 255 255 255 255 255 255 255 255] inf:false size:0} splits:[] thisSize:2113661 dropPrefixes:[]}
W0528 10:04:17.034724 21 log.go:36] While running doCompact: sync p/MANIFEST: file already closed
W0528 10:04:17.566470 21 mvcc.go:148] Error failed when calling List.rollup: while encoding: cannot iterate through the list: cannot initialize iterator when calling List.iterate: cannot read initial list part for list with base key 000000000000000000001b656261792e6c697374696e672e736f6c645f62795f73656c6c6572040000000000001374: could not read list part with key 040000000000000000001b656261792e6c697374696e672e736f6c645f62795f73656c6c65720400000000000013740000000000000001: Key not found rolling up key [0 0 0 0 0 0 0 0 0 0 27 101 98 97 121 46 108 105 115 116 105 110 103 46 115 111 108 100 95 98 121 95 115 101 108 108 101 114 4 0 0 0 0 0 0 19 116]
W0528 10:04:19.196584 21 log.go:36] [Compactor: 2] LOG Compact FAILED with error: MANIFEST removes non-existing table 3752678: {span:0xc00d154c00 compactorId:2 t:{baseLevel:2 targetSz:[0 10485760 10485760 16910574 169105742 1691057427 16910574274] fileSz:[67108864 2097152 2097152 4194304 8388608 16777216 33554432]} p:{level:4 score:1.370733526008833 adjusted:2.142197352896229 dropPrefixes:[] t:{baseLevel:2 targetSz:[0 10485760 10485760 16910574 169105742 1691057427 16910574274] fileSz:[67108864 2097152 2097152 4194304 8388608 16777216 33554432]}} thisLevel:0xc00042c3c0 nextLevel:0xc00042c420 top:[0xc022974780] bot:[0xc0446a9800] thisRange:{left:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 110 38 0 0 0 0 0 0 0 0] right:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 118 97 255 255 255 255 255 255 255 255] inf:false size:0} nextRange:{left:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 99 105 0 0 0 0 0 0 0 0] right:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 118 97 255 255 255 255 255 255 255 255] inf:false size:0} splits:[] thisSize:2267643 dropPrefixes:[]}
W0528 10:04:19.196665 21 log.go:36] While running doCompact: MANIFEST removes non-existing table 3752678
W0528 10:04:19.200899 21 log.go:36] [Compactor: 1] LOG Compact FAILED with error: MANIFEST removes non-existing table 3752679: {span:0xc00a749300 compactorId:1 t:{baseLevel:2 targetSz:[0 10485760 10485760 16910574 169105742 1691057427 16910574274] fileSz:[67108864 2097152 2097152 4194304 8388608 16777216 33554432]} p:{level:4 score:1.3729726516323733 adjusted:2.14569668292102 dropPrefixes:[] t:{baseLevel:2 targetSz:[0 10485760 10485760 16910574 169105742 1691057427 16910574274] fileSz:[67108864 2097152 2097152 4194304 8388608 16777216 33554432]}} thisLevel:0xc00042c3c0 nextLevel:0xc00042c420 top:[0xc034eff8c0] bot:[0xc013279d40 0xc0115c1d40] thisRange:{left:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 80 73 80 0 0 0 0 0 0 0 0] right:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 84 72 82 255 255 255 255 255 255 255 255] inf:false size:0} nextRange:{left:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 77 105 100 0 0 0 0 0 0 0 0] right:[0 0 0 0 0 0 0 0 0 0 17 101 98 97 121 46 108 105 115 116 105 110 103 46 110 97 109 101 2 10 97 32 86 255 255 255 255 255 255 255 255] inf:false size:0} splits:[] thisSize:2230336 dropPrefixes:[]}