During the closing credit sequence with Buackaroo Banzai and the gang walking in the aqueduct, Perfect Tommy is first seen wearing a white jacket and black pants. As they take their final turn in front of the "Buckaroo Banzai" graffiti on the wall, Perfect Tommy is wearing a completely different outfit - gray jacket and red pants.
After Buckaroo briefs the president on the situation, the president replies "I don't know what to say. Lectroids, Planet 10, nuclear extortion, a girl named John?" However, Buckaroo didn't mention John Emdall during his briefing and the president doesn't watch the video until later.
John Bigboote's glasses disappear and reappear between shots when he holds Professor Ikeda in a head-lock.
During the battle at the Yoyodyne plant the shot of one of the
aliens being shot and falling from a catwalk (elevated walkway) is repeated.
When Secretary of Defense McKinley tries to bribe Blue Blazer Irregular Scooter Lindley with a 20 dollar bill, he is distracted by Perfect Tommy and Scooter snatches it out of his hand. In the wide shot following that close up you can still see the 20 dollar bill in McKinley's right hand.
While all of the Yoyodyne employees applied for Social Security cards on 11/01/1938, the "Halloween" broadcast of Orson Welles' Mercury Players occurred on Sunday, 10/30/1938. New Jersey (Jeff Goldblum) incorrectly cites the air date of the broadcast as Halloween (which would have been Monday, 10/31/1938).
During the jet-car test, after they have launched, radio traffic is heard saying "APU start is go". This refers to an auxiliary power unit, a small engine used to run systems and start main engines. This shouldn't be needed after launch. It is also heard prior to launch, and makes much more sense then.
The test car is shown using regular passenger tires which are "S" rated, or can sustain a maximum sustained speed of 112 miles per hour. The vehicle is shown going at the speed of sound, which is about 750 miles per hour, and there is not a tire in the world that can sustain that speed without destruction long before that is reached.
The orderly takes away Dr Lizardo's TV since he "used another 10,000 kilowatts again this month." Electricity is metered in kilowatt-hours (kWh), not kilowatts. 10,000 kilowatt-hours would be 36 gigajoules (GJ) in the International System of Units (SI).
Aboard the bus, a tatami mat floor is seen when the boys are talking about Lizardo and Banzai is meditating. However, such a floor is not to be walked on with shoes, yet the boys are wearing shoes.
When Dr. Lizardo has Penny hostage and is talking to Buckaroo on the phone he says "a Penny for your thoughts" and laughs. At that time Penny spits in his face and he stops laughing, but the sound of his laughter continues. It's actually John O'Connor laughing, though.
At the end of the closing credits, when "Buckaroo Banza!" is seen painted on a concrete wall, erasures marks reveal several attempts to get the text right. (and ironically still got the spelling wrong)
When the two hunters are poking at the thermopod up in the tree, a shower of sparks falls when they hit the pod. You can see the power-cable they used to produce these sparks fall away as the pod slides out of the tree.
When Dr Lizardo is pulled out of the wall after his failed attempt to access the 8th Dimension, the hole in the wall in which he is placed is visible.
During the test car run, the screen says "seeled" instead of "sealed."
A running gag has Buckaroo shocking whoever he touches after he is charged by the Lectroids. When he first touches Penny in the Pitt there is no shock.
The end credit graffiti actually reads "BUCKAROO BANZA!" and not "BANSAI".
During Buckaroo's guitar solo at the night club, he steps over next to the two saxophone players. As they sway together, the camera cuts to a tighter shot of the two sax players. On the left Buckaroo swings his guitar around behind his back (the guitar body visible over his shoulder) getting ready to grab his trumpet, while his solo riffs continue for another five seconds.
As Lizardo discovers Banzai has infiltrated Yoyodyne, he yells to turn off the klaxon sounding the alarm. His mouth says "Goddam klaxon" but what is dubbed is "Gosh darn klaxon".
When Banzai is in the rocket car, and plugs the module in, you can hear them reading out his location as N28º 36' 30.32", W80º 36' 14.8". This is the location of the Saturn causeway at Kennedy Space Center. NOT the middle of a desert, with a convenient mountain to fly through.
New Jersey explains that the Lectroids emit a chemical which humans breathe, and as a result they make us see them as human. However, at that same time, the President is seeing John Parker on television as a human, not a Lectroid, even though he cannot possibly be inhaling the chemical hundreds of miles away.