Why does gitlab backup [SKIPPED] some repositories?

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I'm relatively new to gitlab. I use gitlab-ce 12.8.1. During a backup gitlab-backup create I receive the following information:

user/some-repo ... [DONE]
user/other-repo ... [SKIPPED]

Does anyone have an idea, why some repos are skipped? gitlab-rake gitlab:git:fsck reported only for two of them an error.

user/myrepo on default: 5:GetRepoPath: not a git repository '/var/git-data/repositories/user/myrepo.git'

Any help will be appreciated.

Edit:

I switched to gitlab-ce 12.7.6 and restored an older backup. After that gitlab-rake gitlab:git:fsck reported everything is ok. I think the repos were skipped during backup, because they are empty.

But:

The webfrontend shows for a skipped repo:

Storage: 104 MB (Repository: 104 MB / Wikis: 0 Bytes / Build Artifacts: 0 Bytes / LFS: 0 Bytes)

Switching to the repo shows The repository for this project is empty.

Looking at the file system, there is a ../git-data/repositories/user/repo.git directory with size of 104 MB.

So what's going wrong?

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