Did it blow up in its entirety, with the big whiteout and everything?
Edit: just gave it a quick go and it seems to end properly for me, hmm.
It did, and the main portion is still there in all it's blown up decal glory, dead. Guess I'll try killing it again.
EDIT: Blew it up again, same problem.
Spoiler
Blew up all the gunports, masts, shield, etc., and it exploded leaving the mainbody's husk.
EDIT2: Don't know if it's any different, but I forgot to mention that it's a
Spoiler
Domain-Era Survey Mothership
Forgot to mention it.