Deliberate mistake: In the shot near the end of the film where Donnie grabs the keys for the station wagon, you can see a Blockbuster Video member card in a cup. That card design wasn't used until the mid to late 1990's. This movie is set in 1988. Deliberate as it's a product placement, but still wrong. (01:37:10)
Deliberate mistake: After Carmen rescues Juni on the boat/sub, he accidentally re-engages the autopilot and they submerge. In the next shot as two Thumb Thumbs jump off their speedboat, the name, 'Donzi', that is written across the side of the boat, is backwards. This shot is flipped. (00:24:10)
Deliberate mistake: The energy the meteor would displace upon impact would have created a crater of significant size compared to what was portrayed. It also didn't appear to have any impact to the structure of the cavern it crashed into either.