Only thing similar I've had happen was in a game against a Vasari AI.  After a massive incursion of their forces, I had defeated all of them with static defenses except for 8-10 carriers.  I think because I rebuilt mines on the phase exit out of the system, they decided to just stay still and not move at all for a long period of time.  They kept rebuilding fighters, and because I only had a handful of fighter squads myself left to dispose of them, they just sat there in my well.  They seemed too afraid to leave and without any routines to move around the well or do anything else.

Did you also have mines up or is this just an unrelated but similar story?

That same thing happened to me last night. If it had deployed it's mines and jumped away, it would make sense, but it just sat there, waiting to be destroyed

I have seen all AI races do this in late game stages. Usually after I start slaughtering their scouts regularly(usually with SC). They are a lot tougher and seem to last longer.