We believe we're seeing comments on pull requests being marked as "outdated" when the file/hunk in question hasn't changed. An example is this pull request (this is a private repo, but I hope you can take a peek anyway).
The pull request has two commits and was created yesterday. Today I made several comments in the combined diff view. These comments are now marked with "outdated" even though no new commits were added to the pull request.
The files in question have changed in the main repository, though. I'm not sure if that is the problem, but I had expected that updating the file in the main repository wouldn't invalidate my comments on the pull request.