When Bill is waiting in the car and he sees Alvin stealing money out of a stores cash register, a man with dreadlocks is walking left. When Bill runs out of the car, the same man is seen walking left again.
Agent Peyser's car is blue through most of the movie, then it turns white when it crashes into the tree, then it then turns blue again later.
When Peyser's car hits the tree, only one man can be clearly seen in the car, although there should be four people in it.
The "Bat Boy Found in Cave" National Enquirer front page was published in 1992. This movie was filmed in 1994.
In the closing scene at the bus stop the street in the background is way too clean to have been just after a snow storm.
When the brothers are in the store before the bank robbery, Alvin takes a box of Cap'n Crunch off the shelf and starts eating handfuls out of the box without even opening the bag inside first.
When Alvin is saying good-bye to Merlin the horse, he leans over and kisses him. The kiss sound effect is heard while Alvin is in mid-sentence.
When Alvin picks up Dave and Bill after the bank robbery you can see a crew member to the right of the screen holding his hand up to block traffic in the opposite direction.