Throughout the movie, particularly in the beginning with one of the first fight scenes, He-Man appears to have a gash on his upper chest/shoulder area. It switches from right to left and back again several times.
In the scene where He-Man is running from the Air Centurions, when he goes in the door to the warehouse, his sword and cape fall off his back. In the next frame, when he is running up the stairs everything is in place again.
When Evil-Lyn introduces the bounty hunters to Skeletor, they change position between shots.
During the climactic battle scene at Castle Grayskull, He-Man jumps up onto a high platform and starts running. There is a bad edit, and it cuts to He-Man running before his feet land. There is also no sound of his feet hitting the platform.
When Beastman throws Carl the janitor through the door in the high school, he flies backward, but when the shot cuts to him flying through the door, he's facing the other way.
When He-Man hangs upside down while pursued by Skeletor's Air Centurion, his hair does not hang down. However, since he's "hanging from" an anti-gravity platform, on which he's standing, from his point of view he's standing the right side up. If his hair would fall down (the real down), then his entire body would follow, but that does not happen. Apparently, that's how those anti-gravity platforms work.
The keyboard that Kevin got from the music store seems to play back to front, with the high notes to the left.
The keyboard is seen as it would appear from Teela's point of view, therefore the high to low range of the notes is still correct.
Before He-Man surrenders himself to Skeletor on the roof top, a group of troopers try to subdue him by pinning him down. As they are doing so another trooper runs towards them, trips over a body on the floor and appears to fall into He-Man.
When Skeletor's entourage begin to arrive through the "door", there is a flipped shot - a "Rexall Drugs" is seen clearly in reverse behind the legion marching right to left.
Throughout the movie, Skeletor's nose appears visible through the mask. The light above and red glow beneath bounce off the black paint on his nostrils.
A "stone" statue bounces on the floor when pushed over.
In the fight scene at the music store, the glass shatters before the troops touch it.
At 1:43 when entering a doorway to avoid the sky centurions, He-Man's sword falls from his back, but in the next scene it's back where it should be.
At 18:03 when Gwildor gets thrown in the mud coming out of the portal he doesn't have any mud on his hair, face or ears. Hair barely looks wet especially considering the mop he has.
In the beginning when soldiers are carrying Gwildor in the net and He-Man comes along and kills them all you can see Gwildor is awake in the net yet he doesn't cry out for help and sits quietly while He-Man walks off and has a whole conversation before he starts asking for help. Once he sees He-Man is an ally by knocking his captures down he wouldn't wait to ask for help especially when it looked like He-Man could be walking away.
During the attack on the school, Karg says, "She might know where the key is", to his troops yet his mouth does not move.
At the final battle between He-Man and Skeletor, He-Man shouts out "I have the power!" as he pulls the sword out of the anvil. You can clearly see that he mouth does not match what he shouts.
Shortly after the half-of-a pink Cadillac arrives in Eternia, the small stands holding up the rear of it are visible against the floor.
When Karg leads Skeletor's troops charge into Gwildor's home, he tells his men to "find the key". It is impossible for him to have known about a second cosmic key as his superiors did not even know until shortly later on.
When Gwildor asks Kevin and Julie if there's any point in time they wish to go, Kevin says to just send them both home. As Julie and Kevin go through the portal that Gwildor opened, Julie quickly turns around and tells Gwildor to send them back. Before she can say anything else, Kevin drags her into the portal. Julie then wakes up in her bed and finds she had been taken back to the day her parents died. There's no way Gwildor should have been able to do it since he knows nothing of the death of Julies parents or when they died.
When Skeletor and his army invade the city on earth trough the dimensional gate, the whole invasion and hundreds of alien soldiers do not seem to attract any attention from law enforcement or citizens. The streets seem to be deserted and empty.
Skeletor uses the phrase "the Alpha and the Omega." It seems unlikely a warlord from another planet would know the letters of the Greek alphabet, or to use them in a Biblical context.