After the other three Ghosbusters leave to search for Slimer, Peter is left standing alone in his pajamas. His hair is a lighter shade of brown normally associated with Ray Stantz. It returns to his normal darker shade in the next shot when he turns around.
Peter is the first to retrieve his proton pack during the final battle. As he fires at the ghost ringleader, the other three run past him, but are colored as if they are random bystanders. What is more, one of them is drawn much larger in the frame, and should have been layered in front of Peter and Slimer, but is layered behind them, making him appear to be a giant.
When the Ghostbusters are 'taking the long way home' back to headquarters, their logo on the passenger side door is flipped horizontally.
In the scene with the street thugs, the character with the sunglasses switches position with his mo-hawked friend, who suddenly appears standing in front of Egon even though he was walking along side with him the moment before, before switching back into the character with the sunglasses.
In the opening scene, the ECTO-1 license plate mistakenly read, ECTD-1.
When Janine reads the note Slimer left behind, her eyes are misaligned.
In the first scene, Winston and Egon are in the back of the ECTO-1. When Winston's leg and arm are shown from the back, his hand is Caucasian and his flight suit the colors usually associated with Ray Stantz.
When Egon is lying on his back in the ECTO-1, pointing in which direction they should go, the others are seen walking away from his point of view. But Winston (who is furthest from the camera) is painted in Egon's color palette.