When you use special-unload, a menu pops up in the lower left with a list of ships to unload.
If there's a lot of ships on the list, then the next-to-last one overlaps the buttons like map/stats/ctrls/shiptypes. If you try clicking the next-to-last ship in special unload, it clicks the overlapped button instead, and you can't unload that ship.
(Also, it would really be nice if mousing over a ship in the transport would pop up the info box. When I've got a pile of ships in a transport, I'm often searching through them for 'what can I kill refractive armor with'.)
This would go in mantis, but...apparently it's not sending out emails for account creation, and I wanted to post it somewhere before I forget about it.