Continuity mistake: There are a couple of instances in the movie where the models do not correspond with the actual sets. When Klytus arrives at the Hawkmen city he lands near the top of the city. Yet in that very hall there is a pit with a deep void underneath. Such a room could only exist at the bottom of the city. Also, when the Hawkmen start to land on Ajax, its engine section appears to be missing.
Revealing mistake: Just after Klytus has his sticky curtain call, and King Vultan orders the evacuation of the Sky City, watch for the wide shot with the fleeing Hawkmen superimposed in the background. As Vultan tells our heroes he and his men have too much to carry to give them a ride, watch his entire multitude of brave fleeing Hawkmen suddenly disappear one frame before the next shot cuts in.
Other mistake: The scenes with Flash and Aura in the shuttle are a complete mess. She tells him that the left lever controls direction, the right controls the altitude. When they are passing the planet Aquarius, she tells him to take a left turn over Fridgia. A) They are passing Aquarius at the time, not Fridgia. B) He moves the right lever instead of the left lever. C) The craft doesn't change direction or altitude and even if it had moved left as supposed to, they would have ended up crashing into Aquarius. The scene when Flash wants to talk to Dale is even worse. He pulls down the left lever to dive into Fridgia. It is the wrong lever. Then when he pulls back up, he correctly uses his right hand, but the right lever is already in the up position as seen in the previous shot.
Continuity mistake: When Flash is restrained in Ming's dungeon, he has a spiked headpiece on, preventing him from seeing. The spikes on this headpiece change position from shot to shot during this sequence in relation to his tied-up arms - i.e. the headpiece keeps being turned, and then is back in position again depending on the shot.
Revealing mistake: Just after Vultan evacuates War Rocket Ajax leaving Flash on board, there is a shot of the rocket heading towards the camera. There is a green-tinted box surrounding it that the special effects team forgot to remove, after it had been rendered against the background.