1. In the save dialog box, if you scroll sideways, frequently it scrolls out of control all the way to the end of the folder list when you only tried to go one or two pages over.
2. Also in the save dialog box, sometimes double-clicking on a subfolder will cause the file to save immediately to the current folder.
3. The cookies file randomly deletes itself, losing all logins and web site customizations. (EDIT: This is a bug with the TorButton add-on, not Firefox)
Not bugs, but annoying:
Fasterfox, Linkification and