Finding conflicts in a PR between two branches that can merge cleanly if I do it locally.

Not letting you resolve conflicts in the UI if the source branch is protected, even though the UI gives you the option to commit the resolution to a new branch if you do it for an unprotected source branch.

Updating the source branch in the PR if you choose to do the above - something you can't do yourself!

Not showing branches in a hierarchy (as if they were directory paths)