Yip, Giles explained what happened.... Here:
PostPosted: Wed Jan 18, 2006 2:54 pm
I think this is down to the Behemoth targeting a Thargon and, when the Thargons go uncontrolled, continuing to try to engage it.
This blocks the Behemoth from reacting to docking requests, and hence both you and all the Navy ships have to wait idly by.
I've been looking at the problem (last time a few weks ago) - I guess I need to look again.
Next time, try pausing the game and pressing '0' (zero), this'll dump a list of entities and their AI states to the console. Then email me the output - it may help.
(Edit:) With GalCops, probably similar: chasing a baddie, and it ejects, so ship becomes uncontrolled entity, AI confused etc...