In releases prior to 3.30.0, I had noticed that the Packages index in the metadata folder wasnt properly updated depending on whether you did the package upload via the API vs a web UI upload (it would only consistently update the index if things were uploaded through the API only but mixing the two caused it to lose track of the deb's in the repo and require re-uploading).
This seems partially fixed as of 3.30.0 but I have seen instances where the uncompressed Packages file doesnt match the contents of the compressed Packages files in the same folder in the metadata for the repo. This may not be much of an issue because I think most things tend to pull one of the compressed forms, but if you go to manually look at it to just verify what it thinks is there, it could be off.
Another thing I noticed is that if you manually delete the metadata folder from the apt repo, going into the repo settings and pressing 'Rebuild Index' button does not cause it to regenerate the metadata folder, but rather its only recreated on the next deb package upload. Im not sure if thats expected behavior or not.