When Link and Stoney are in the convenience store and steal the Squishy from the machine, Link has it all down his shirt when they leave. When Link returns the shirt has no marks on it at all.
The ICEE stain on Link's shirt when he returns the stolen pair of sunglasses.
When the teacher writes on the board, he puts a comma between "Cro-Magnon" and "Man". When the chart flips, the comma is gone.
When Link and his girlfriend are trapped by the cave in, Link is wearing a sort of crude hide shirt or jacket. When he comes out of the ice, he is only wearing a loin cloth.
The napkin on Encino Man's shirt disappears and reappears throughout his dinner with the family.
When Dave and Stoney first discover the block of ice Link is frozen in, Dave knocks on it and it makes a hollow noise. However, the block of ice should be completely solid and therefore, not sound hollow.
No man can be held up by staples.
At the prom, a microphone is aimed at the head of the bass guitarist's stack. The sound comes out of the speaker cabinet underneath it, so the microphone should be about a foot lower.
When Link and Stoney are on their way to Spanish class, Stoney says "La día es mi hermanos - The day is beautiful" which is incorrect. 'La día es mi hermanos' translates to 'the day is my brothers.' The correct translation of 'the day is beautiful' would be 'el día es hermoso.'
The translation given has the incorrect gender in the spanish translation.
When Dave's mom asks Link if his necklace is old, Link nods in the affirmative. If Link was a caveman and still had very limited speaking skills, he wouldn't be able to comprehend the question. He also wouldn't comprehend "I'll be back" or "Wheez the Juice," which he saw people do. He could've seen someone nod and mimicked it at (unknowingly) the right time and right place.
The high school-aged characters are seen drinking in a bar and from a keg of beer. Since the reversal of Prohibition, the legal drinking age in California has always been 21. However, no one checks their IDs and it is possible for high school kids to get their hands on alcohol through fake IDs or other means.
When David jumps into the car that Link is driving, you can see the stuntman's face.
After Stoney and Dave clean up the caveman, they take a Polaroid picture of themselves. Their pose when the camera flashes, is clearly different from the actual picture. Most notably, Stoney's face.
When Dave and Stoney jump into the hole the rocks move like they are hollow.
When Encino Man drives a car on two wheels, you can see a wire holding up the car.
The convenience store where Stony and Link stock up on junk food says Food 7 Mart on the exterior shot. Inside, you can clearly see it is a Circle K, most notably, the wall ads for "Thirstbusters" as well as the wallpaper near the ceiling.
When David climbs up the pool ladder, his mother bends over to talk to him. The crew and camera equipment form a clear shadow on her back.
When Link and the guys first enter the school, the cameraman is reflected in the glass door that Link runs into.
Stony says Matt has 18-inch biceps. Arnold Schwarzenegger's arms were 22 inches at his competitive prime. It's very unlikely that even a large high school student (which Matt clearly isn't) would be so muscular. Stony said his own arms were 4 inches, so he may have been exaggerating.