Some backups don't contain all repositories

Title says it all, some of our backups are missing some of our repositories. I have not been able to discern a pattern in which repos are included and which ones aren't, but it's always the same ones missing.

Backups created with docker exec --user git -it gitlab_gitlab_1 bundle exec rake gitlab:backup:create are always complete, only the automated backups show this behaviour.

Our automated backup settings:

        - GITLAB_BACKUP_SCHEDULE=daily
        - GITLAB_BACKUP_TIME=23:00
        - GITLAB_BACKUP_EXPIRY=0

We are running sameersbn/gitlab:9.5.5.

Please advise what further info we can provide and/or how we can debug this issue ourselves, as we could find no log files related to the backup process.

Start by comparing the automated backup path with the manual docker exec --user git -it gitlab_gitlab_1 bundle exec rake gitlab:backup:create command. Review the provided GITLAB_BACKUP_* settings and container output or logs to find where automated backups omit repositories. Done means identifying the cause and confirming that automated backups include all repositories.