Awesome springs to mind. Wouldn't let you get past the second planet.
Elite II had a problem with the autopilot but it was easily rectified by advancing time to the fullest.
Eye of the Beholder II had a strange bug with the 9 pressure plates. I think it was located in the ant level...a place where you couldn't go to sleep due to nightmares??? Long time ago...
Captive was another one. Mr Captive man will agree, I'm sure
If you got to Base 2 Station 3 you couldn't insert a certain card because it was behind the door you had to get past. luckily later, people wrote in about it and it was made accessible by Amiga magazines. Hmm..I thought the flying lizards were bad, nothing compared to the lightning quick black trolls.