Yeah, I've had this issue. The cargo list doesn't scroll like the system components or inventory.
http://steamcommunity.com/app/445220/discussions/1/135508031949038521/
This is a phantom fighter bug.
http://www.avorion.net/forum/index.php/topic,940.0.html
Apparently if you have up/down facing hangars, this can happen and apparently also fixed in the beta branch.
Sectors with many asteroids seems to be the worst offender and trigger the fps drop. Jumping out of that sector seems to help with the fps but only temporarily.
Fighters have very bad pathing and don't always return, which can trigger phantom fighter bug. Turning the ship doesn't do anything to help with the recall.
http://steamcommunity.com/app/445220/discussions/1/135508031948570852/
I'm having a similar issue in addition to fighters not landing. If fighters don't recall completely, launching the remaining ones will cause more to become phantom and lost.
http://steamcommunity.com/app/445220/discussions/1/135508031948570852/