Continuity mistake: The head of Mega-Maid mysteriously shrinks in size. After Spaceball-1 transforms into Mega-Maid, the head is gigantic enough for a Winnebago to fly through for a considerable length of time. However, later on in the film, after the head has been jettisoned and crashed on a beach, the head is only big enough to hold a few dozen people. This can be determined by the size of the people coming out of her nose.
Continuity mistake: Near the beginning of the movie, Milla Jovovich reads a note that has been left on the desk. She didn't write it, as they demonstrate in the film. However, when they do show the person who wrote the note composing it, the handwriting is different from that in the note from the earlier scene. (00:10:20 - 01:12:25)
Plot hole: In all scenes where special or heavy items are used against the sixers, they are 'zeroed' in waves or circles. This can be seen by their stations turning red in clusters. This makes no sense as the stations have fixed positions, meaning that the sixers would have identical positions in the Oasis and have no freedom or own will to move relative to each other.
Continuity mistake: Carmen is wearing white sneakers riding with Juni on the magnetic transporter. After jumping off the magnetic rider and entering the hidden temple, Carmen is wearing black sneakers.
Continuity mistake: The whole time sequence in the last part of the movie is messed up. After trying to nab the bad guys at the hotel, Tom Selleck goes home and puts his son to bed, then is called back in to work, and then the rest of the film is supposed to be the same evening, but it was already late night.
Continuity mistake: When Marlon stocks the vending machine, the camera (inside the back of the machine) shows him stocking the 1st row with brown-wrapper candy bars. He starts stocking the 2nd row with yellow-wrapper bars; Truman interrupts him for a minute (during which Marlon doesn't touch the bars at all). When Marlon continues, the yellow bars have changed to something darker (it's not just a different camera view; even barcodes are different). After another brief interruption, Marlon continues again, and the yellow bars are back. (00:35:00)
Other mistake: Towards the end of the movie, when Superman drops Gus off at the coal mine, Gus begins talking with the coal miners about him and Superman. He then rips open his shirt (as if he had a Superman costume on underneath). How did Gus know that Clark Kent tore his shirt like that in order to change into Superman, or keeps his suit under his clothes at all? The only people who know this fact are the ones who have seen the transformation from Clark to Superman, i.e. the audience.
Continuity mistake: Both Gabe and Yulaw have their hair parted on the right side. But during the fight between them, you can tell they flipped the image of the film as it shows Yulaw's part on the left side in one shot, and again a couple shots later. It then returns to his right side. (01:11:35)
Factual error: The type of surgery shown made by the machine transversely cuts the rectus abdominis muscles. Besides not being a standard surgical incision in order to "remove a foreign body" as stated, it seriously damages important muscles of the abdominal wall making any immediate active mobilization of the trunk virtually impossible, even under strong analgesia.
Plot hole: The first time they communicate with the "entity" in the spaceship, they find a correspondence between numbers sent by the entity and letters of the alphabet. The entity presents itself as "Jerry". Later on, the entity tells Dustin Hoffman, "Stop calling me Jerry" - and then Dustin Hoffman realizes that the number-letter correspondence was wrong, and the actual name of the entity was "Harry". But if that is true, how could they have communicated without problems before? The very first word that the entity used was "hello", which would have to be displayed wrong, since it begins with an "h" and has an "e".
Character mistake: In the scenes in San Diego, all the scenes outside the sub are taking place during daylight hours. Immediately after the crewman relays the message about the mysterious telegraph transmission, the scene shifts to the sub. The commander asks what time it is in Melbourne and is told it is 1500 hours (3PM). But if it were that time in Melbourne, it would be 10PM in San Diego, and thus not during daylight hours. (01:33:30 - 01:38:05)
Continuity mistake: After the bird of prey first fires on Enterprise, Kirk is thrown right out of his chair to his left and lands on the floor. The camera pans around the bridge briefly, seeing the rest of the crew staggering and holding onto things. In the very next shot Kirk is back in his chair shouting "back off, back off" and the crew back in their positions as if nothing has happened.
Continuity mistake: When Claire and Franklin are in the rolling sphere, the door closes and locks. In the next shot, it closes and locks again. (00:43:10)