Deliberate mistake: At the elephant graveyard, little Simba claws Shenzi in the face. When Mufasa saves Simba from the hyenas, the cuts are gone, a few seconds later. [This was done intentionally, I'm sure, for two reasons. The first being, Disney doesn't let fresh scars linger on the screen too long. Secondly, during that same scene when Mufasa rescues Simba & Nala, he claws Banzai in the rear. To stress the point later in the movie, that severe scar is shown too, but only briefly, it too disappears because of reason 1. Still a "mistake", but there's why.] (00:21:50)
Deliberate mistake: After the trilithium missile hits the sun, it is shown going out in real time from Veridian III. As the planet is relatively earth-like, it is several light-minutes away from the sun. The filmmakers wanted it to be obvious that the missile was successful, so they ignored the speed of light. (01:20:35)
Deliberate mistake: In the scene where the bad guy is attached to the missile and fired, in the split second before it hits the helicopter you can see below it a building called SUN BANK, but the letters are backwards. A close look reveals the likely reason - to the right of the reversed building is one which looks just like the building to the LEFT of the Sun Bank building behind the harrier a few seconds earlier. Most likely they couldn't film the chopper from the right side because there was a building there (the one the camera flies through), so they filmed it from the other side (the same side they'd filmed the harrier from), catching the "Sun Bank" behind, then had to flip it to have everything facing the right way. (02:06:55)
Deliberate mistake: Vega's claw never actually hits any of the furnace buttons, but it opens up anyway.
Suggested correction: The claw penetrates the panel cover and most likely shorted the wires inside. You don't have to actually press any buttons to activate it if you short the wires.
Deliberate mistake: When Wade "hits" Roarke for telling his parents about the gun, it's very obvious that his hand doesn't come near the boy's face.
Deliberate mistake: While Jimmy and Billy are being chased by the jet skis one of the baddies fires a missile, and when it lands in the water the long shot is flipped, note "AKZO" is backwards. (00:49:25)