I've been in contact with support for some time about my bibliography not autogenerating. Here's the deal: saving in iCloud Drive prevents this from working. I've had other apps have similar issues with OneDrive, so I suggest saving to a local drive for now and backing up to the cloud.
FYI: Saving in iCloud Drive prevents bibliography from working
It's not impossible, but the causal relationship between the two is not very clear. We'll investigate.
Note also that we fixed an issue which would more generally affect saving to network and other non-default disk volumes some days ago, so make sure you get the most recent 1.0.10 version.
CEO & Co-founder of Manuscripts.app Ltd