Another is that when some rooms get updated, you can get unread notices from the old room and your client keeps telling you that you have new messages even if you don't.

Another thing that I think should be considered a bug, is that when you enable encryption in a room and you have multiple devices on the same account, you have to approve all your devices separately so that they will be able to decrypt the messages...

There are more bugs related to how the encryption process works and I stopped using encryption because of it (some might have been fixed by now...)