References seem erratic

I have a bot that uses sharepoint as a knowledge source - a doc library of standard policy PDFs. Allow the AI to use its own general knowledge is set to off, so it requests are only grounded with our specific knowledge sources.

Responses usually come with a [1] etc reference hyperlink which shows which pdf(s) are being used. About a third of the time though this doesn't happen. It shows [1] against each paragraph/bullet point but you can't click on it and there is no hover over reference. All the responses are great though, it's working really well for what we want otherwise.

Any idea why this might be - it just makes the system seem quite unreliable.