Two that I can remember vividly:
1. When i used the Can on the train in the second movie(I had to go back in time to get the can because I didn't have it, ie I finished two of the movies before getting to that part) The can placed itself below the floor so it looked like they got sucked into the floor. It got back into place after the animation was done.
1.5 When I used the can of nuts in front of the daughter and father molemen on the train it did not play it's sound effect.
2. Do not and I repeat do not get the Opposite sex curse and then the bad luck curse at the same and then wait for the Opposite sex curse to die out. Even though it said the curse was gone the animation was still there and when I got the bad luck curse removed I still had the opposite curse animation floating around. When I clicked the Grampa Moleman dialog option Benny's Curse I got a dialog circle with no dialog(ie I had no choice and could not right click out). Have to go back and do it again.