When `restic check` reports that there are pack files in the repository that are not referenced in any index, that's (in contrast to what restic reports at the moment) not a source for concern. The output looks like this:
$ restic check
Create exclusive lock for repository
Load indexes
Check all packs
pack 819a9a52e4f51230afa89aefbf90df37fb70996337ae57e6f7a822959206a85e: not referenced in any index
pack de299e69fb075354a3775b6b045d152387201f1cdc229c31d1caa34c3b340141: not referenced in any index
The message means that there is more data stored in the repo than strictly necessary. With high probability this is duplicate data. In order to clean it up, the command `restic prune` can be used. The cause of this bug is not yet known.