i've met this several times now but can't reproduce it in a direct way, seems to be random.
The problem is the following my Nexus class ship is loaded with some cargo (cargo expansion installed). About 200 units of cargo are loaded and there are about 20 units of space left. After scoping an ejected enemy pilot the pilot is in the cargo space behind a wall of cargo. If i switch into the combat mode i can't attack the enemy but i'm also stuck in the combat mode.
Don't know whether this is specific for the Nexus class ship i used or if it occurs on others too, but only saw it there.