The Real Ghostbusters has an end sequence, but if you complete the game it gets stuck in the high score table code and you can't do anything (except reboot). If you fail to complete the game, the high score routine works.
Summer Camp was duplicated with some corrupt data causing the music to play bizarre samples. Don Adan fixed this by copying the correct samples from another game (as Dave Lowe reuses several samples in a lot of his games!)
Afterburner also suffers from a corrupt sample problem. Track 15 was duplicated badly causing sound corruption.
Puzznic has a faulty palette while loading the title screen, one of the palette entries was missed so the colours are bizarre. Shifting the table by one word fixes the problem.
There are also a few games that hit the kickstart 1.2 ROM routines directly thus consigning them to only working on kickstart 1.2. They do things like assume a routine is at a particular address or that the topaz font is at a certain memory address.