In the opening scene, Stuart is removing new comics from their shipping box, to the left of the cash register, and putting the stack of books on the counter to the right of the register. After the next cut-away, the box has moved to the right side, into the space Stuart was using to check in the books.
In the comic book store the guy with glasses and an orange stripe on his sweater walks from left to right across store behind Leonard. Scene cuts to Stuart heading over to speak to Leonard and the guy is shown repeating the move from the same starting point.
When the meatloaf falls from the ceiling and lands on the coffee table, it bounces to the edge of an empty space on the table. In the next shot, it's sitting directly in the middle of the empty space.
When Leonard talks with Penny about dating Stuart, the way he holds the mail changes between shots.
When Leonard and Stuart discuss dating Penny, Captain Sweatpants can be seen walking past Stuart. When Sweatpants is (more or less) level with Stuart, the camera angle changes and he's suddenly a foot or so behind him.