At the end Superman burns off the water from a flooded city by burning it into mist with his heat vision...which is pretty much what got the Flash into trouble in the first place.
The narrator says the Justice League is "desperately trying to escape the Fearian forcefield" after they have already escaped a couple of minutes earlier.
Among the animals Aquaman summons in the South Pacific is a killer whale - a sea-going mammal found only in chill waters.
Aquaman flooding the coastlines wouldn't cause palm trees to grow to full height within hours.
When Wonder Woman ties Cheetah up on the rafter with her magic lasso, the star on her tiara is briefly colored purple.
Even though the SuperFriends are immobilized by a device that's supposed to restrict their muscle movement, they're still able to speak, moving their lips in the process.
When Bizarro Alfred sets the Batmobile on automatic to dispose of Batman and Robin, the car's insignia is inverted (a gold bat in a black oval) before becoming normal as it drives off.
The altered Bizarro that tries to dispose of Superman with a street sweeper was wearing a short-sleeved shirt. But after Superman traps him in a phone booth, he has a long blue sleeve exactly like his.
When the disguised SuperFriends enter the Hall of Justice, one of them is wearing a Bizarro costume with an inverted insignia (a yellow backward "S" inside a red shield).
It's a bit odd that when the disguised Superfriends showed up at the door of the Hall of Justice, none of the Legion members thought it was strange they were all wearing full Bizarro Superman and Cheetah costumes, when all the other people who'd been changed had kept their normal clothes while just getting Bizarro and Cheetah heads.
In several shots of the Superfriends when the cell flies through space, there's no roof on the cell.
Batman and Robin summon Alfred to bring another powerpack for the Batcomputer, and are surprised to find that he's been transformed into a Bizarro. Uh, every other man on Earth has also been transformed into a Bizarro, is there some reason why Alfred wouldn't have been?
Although Green Lantern says his ring can't work on their cell because it's yellow, the animators forgot to color it yellow.
So...the Legion of Doom frame the Superfriends by controlling them in their sleep to commit super-robberies, so that they'll turn themselves in, so that they can enter a Legion of Doom trap-cell. Why doesn't the Legion just control the Superfriends in their sleep to enter the cell and then send them off to the sun?
The Batmobile goes down a road to plunge off a cliff. The road ends at the cliff - who the heck builds roads that just lead right up to a cliff and stop?
How does Hawkman hide his wings underneath his Bizarro costume? Or his helmet, come to that?
Superman uses Luthor's dream machine to take control of the awake Legion of Doom, although earlier Lex said it would only work on sleeping targets. And if it works on anybody, awake or sleep, why didn't Luthor use it when the Superfriends revealed themselves at the end?
The dream machine grows substantially between the beginning of the episode, and later when the Superfriends use it on the Legion.
Batman uses the same button on his belt to release a sphere to imprison Bizarro that he used earlier to fire the emergency rockets on the Batmobile.
It seems odd that neither Superman the newspaper reporter, or Bruce Wayne the multi-millionnaire (who can presumably afford a newspaper or two) are unaware of the infamous robberies of Fort Knox and all until they show up at the Hall of Justice and find out about it on the screen.