bug
This error is really annoying. I've been trying to hunt it down without any luck really. Visited the ship probably close to a hundred times with different setups but always seems to return just fine for me.
Do you remember if the cap was visible on the uncollector ship after exiting? Did he do the jump animation back to your ship?
And of course any potential differences you might have noticed between those times it happened and those where it didn't.