They wouldn't remain and seem to cause an issue with ensureDefaultConfig or something default config related.
Here's some logs from a failing run which had some additional logging
<details><summary>Failing log</summary>
```
proc [kibana] spawing 3 calls to setupIngestManager
│ proc [kibana] has setupIngestStatus. is pending
│ proc [kibana] has setupIngestStatus. is pending
│ proc [kibana] has setupIngestStatus. is pending
│ proc [kibana] after await setupIngestStatus
│ proc [kibana] before promise.all
│ proc [kibana] after await setupIngestStatus
│ proc [kibana] before promise.all
│ proc [kibana] after await setupIngestStatus
│ proc [kibana] before promise.all
│ info [o.e.c.m.MetadataMappingService] [JFSIII.local] [.kibana_2/d9f18zusTYONXlP_UrRRCQ] update_mapping [_doc]
│ info [o.e.c.m.MetadataMappingService] [JFSIII.local] [.kibana_2/d9f18zusTYONXlP_UrRRCQ] update_mapping [_doc]
│ info [o.e.c.m.MetadataMappingService] [JFSIII.local] [.kibana_2/d9f18zusTYONXlP_UrRRCQ] update_mapping [_doc]
│ info [o.e.c.m.MetadataMappingService] [JFSIII.local] [.kibana_2/d9f18zusTYONXlP_UrRRCQ] update_mapping [_doc]
│ info [o.e.c.m.MetadataMappingService] [JFSIII.local] [.kibana_2/d9f18zusTYONXlP_UrRRCQ] update_mapping [_doc]
│ proc [kibana] after promise.all. get config.id config1
│ proc [kibana] after promise.all. get config.id config1
│ proc [kibana] after promise.all. get config.id config1
│ info [o.e.c.m.MetadataMappingService] [JFSIII.local] [.kibana_2/d9f18zusTYONXlP_UrRRCQ] update_mapping [_doc]
│ proc [kibana] setupIngestManager error { Error: [ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1]: [version_conflict_engine_exception] [ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1], with { index_uuid="d9f18zusTYONXlP_UrRRCQ" & shard="0" & index=".kibana_2" }
│ proc [kibana] at respond (/Users/jfsiii/work/kibana/node_modules/elasticsearch/src/lib/transport.js:349:15)
│ proc [kibana] at checkRespForFailure (/Users/jfsiii/work/kibana/node_modules/elasticsearch/src/lib/transport.js:306:7)
│ proc [kibana] at HttpConnector.<anonymous> (/Users/jfsiii/work/kibana/node_modules/elasticsearch/src/lib/connectors/http.js:173:7)
│ proc [kibana] at IncomingMessage.wrapper (/Users/jfsiii/work/kibana/node_modules/elasticsearch/node_modules/lodash/lodash.js:4929:19)
│ proc [kibana] at IncomingMessage.emit (events.js:203:15)
│ proc [kibana] at endReadableNT (_stream_readable.js:1145:12)
│ proc [kibana] at process._tickCallback (internal/process/next_tick.js:63:19)
│ proc [kibana] status: 409,
│ proc [kibana] displayName: 'Conflict',
│ proc [kibana] message:
│ proc [kibana] '[ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1]: [version_conflict_engine_exception] [ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1], with { index_uuid="d9f18zusTYONXlP_UrRRCQ" & shard="0" & index=".kibana_2" }',
│ proc [kibana] path: '/.kibana/_update/ingest-agent-configs%3Aconfig1',
│ proc [kibana] query: { refresh: 'wait_for' },
│ proc [kibana] body:
│ proc [kibana] { error:
│ proc [kibana] { root_cause: [Array],
│ proc [kibana] type: 'version_conflict_engine_exception',
│ proc [kibana] reason:
│ proc [kibana] '[ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1]',
│ proc [kibana] index_uuid: 'd9f18zusTYONXlP_UrRRCQ',
│ proc [kibana] shard: '0',
│ proc [kibana] index: '.kibana_2' },
│ proc [kibana] status: 409 },
│ proc [kibana] statusCode: 409,
│ proc [kibana] response:
│ proc [kibana] '{"error":{"root_cause":[{"type":"version_conflict_engine_exception","reason":"[ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1]","index_uuid":"d9f18zusTYONXlP_UrRRCQ","shard":"0","index":".kibana_2"}],"type":"version_conflict_engine_exception","reason":"[ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1]","index_uuid":"d9f18zusTYONXlP_UrRRCQ","shard":"0","index":".kibana_2"},"status":409}',
│ proc [kibana] toString: [Function],
│ proc [kibana] toJSON: [Function],
│ proc [kibana] isBoom: true,
│ proc [kibana] isServer: false,
│ proc [kibana] data: null,
│ proc [kibana] output:
│ proc [kibana] { statusCode: 409,
│ proc [kibana] payload:
│ proc [kibana] { message:
│ proc [kibana] '[ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1]: [version_conflict_engine_exception] [ingest-agent-configs:config1]: version conflict, required seqNo [274], primary term [1]. current document has seqNo [275] and primary term [1], with { index_uuid="d9f18zusTYONXlP_UrRRCQ" & shard="0" & index=".kibana_2" }',
│ proc [kibana] statusCode: 409,
│ proc [kibana] error: 'Conflict' },
│ proc [kibana] headers: {} },
│ proc [kibana] reformat: [Function],
│ proc [kibana] [Symbol(SavedObjectsClientErrorCode)]: 'SavedObjectsClient/conflict' }
│ proc [kibana] setupIngestManager ok
│ proc [kibana] setupIngestManager ok
│ proc [kibana] has setupIngestStatus. is pending
│ proc [kibana] after await setupIngestStatus
│ proc [kibana] before promise.all
│ proc [kibana] after promise.all. get config.id config1
│ proc [kibana] setupIngestManager ok
│ info [o.e.x.s.a.r.TransportPutRoleAction] [JFSIII.local] updated role [fleet_enroll]
│ info [o.e.x.s.a.u.TransportPutUserAction] [JFSIII.local] updated user [fleet_enroll]
│ proc [kibana] setupFleet before getDefaultOutputId
│ proc [kibana] setupFleet after getDefaultOutputId aed7a97e-9212-4ff9-b562-8b45f085f0d6
│ proc [kibana] setupFleet before updateOutput aed7a97e-9212-4ff9-b562-8b45f085f0d6 { fleet_enroll_username: 'fleet_enroll',
│ proc [kibana] fleet_enroll_password: 'OWE3MTM3NzMtZDM4Zi00OGUwLWFkYmMtZDMwNzE0YjMwMGY2' }
│ proc [kibana] setupFleet before generateEnrollmentAPIKey { name: 'Default', configId: 'config1' }
│ proc [kibana] server error [09:30:33.314] Error: Internal Server Error
│ proc [kibana] at HapiResponseAdapter.toError (/Users/jfsiii/work/kibana/src/core/server/http/router/response_adapter.ts:129:19)
│ proc [kibana] at HapiResponseAdapter.toHapiResponse (/Users/jfsiii/work/kibana/src/core/server/http/router/response_adapter.ts:79:19)
│ proc [kibana] at HapiResponseAdapter.handle (/Users/jfsiii/work/kibana/src/core/server/http/router/response_adapter.ts:74:17)
│ proc [kibana] at Router.handle (/Users/jfsiii/work/kibana/src/core/server/http/router/router.ts:263:34)
│ proc [kibana] at process._tickCallback (internal/process/next_tick.js:68:7)
```
</details>