As we'll find out in the "History of Doom" episode, Lex Luthor became a bald supervillain because of Superman's intervention as Superboy. So with no Superman, how did Lex ever become his villainous self? Ditto for Bizarro, who is a faulty duplicate of Superman himself. Even if the Legion is immune from having their memories altered, wouldn't the Superfriends wonder who that Bizarro guy in a Superman outfit is?
When the escaping Superfriends bring up the Legion's computer files, the picture of Green Lantern shows his costume is entirely the darker green of his inserts.
When Superman rescues the imprisoned Superfriends, among them is Green Lantern...who is at the same time outside anchoring the Legion of Doom ship. It should be Aquaman among the prisoners - GL is in his place.
In the first shot of the Hall of Justice, right before the Legion launch their attack, Hawkman's leggings are flesh-colored rather than their typical green.
So apparently Lex didn't watch all of Superman's origins, or he'd know that the Kents found him as an infant, revealing his secret identity as Clark Kent.
After the SuperFriends return to the Hall of Justice from Saturn, Superman's cape has a red "S" inside a yellow shield (it should be entirely yellow) when they're viewing the giant Legion members on the viewscreen.
When Batman's utility belt defrosts the SuperFriends from their icy stasis on Saturn, the green pants portion of Hawkman's outfit is missing.
When the Legion of Doom members start to grow they're standing inside the Hall of Justice. When we see them growing in the next shot, they appear to have been standing behind it.
Green Lantern is in charge of carrying any teammates who can't fly or survive in space when they go to different planets like in "World's Deadliest Game." Is there some reason why he didn't just do that and start flying home when they escaped the ice on Saturn? Did they think they'd find the secret to beating the Giants of Doom there or something?
When giant Superman defeats giant Bizarro, the villain is pushed behind the pillars of the Lincoln Memorial to imprison him. Bizarro would be more than strong enough to smash stone columns at normal size, though, let alone after growing to a hundred feet tall.
Why did Captain Cold freeze the Parthenon before Toyman started digging for the element for Bizarro's growth ray? It didn't really seem to accomplish anything, and frozen ground is a lot harder to dig through.
Giant Green Lantern traps giant Sinestro in a large green bottle conjured up by his ring. But since Sinestro still has his, and his yellow energy always trumps Green Lantern's, why does he just sit there and accept defeat?
Just after Superman, Batman, Flash, and Green Lantern are enlarged, Flash says they can now put an end to the Legion of Doom's plans for conquest. But just as they split up upon departing the Hall of Justice before the next scene, Robin--not Flash--is seen as one of the giant SuperFriends.
When the Flash stands next to the frozen and defeated Captain Cold, a significant portion of his left glove seems to be missing, leaving his fingers bare.
When four of the Superfriends are hit by the duplicate growth ray to battle the giant Legion of Doom members, Batman's insignia logo is briefly reversed--that is, a gold bat inside a black oval, instead of the familiar black bat inside a gold oval.
When the Superfriends are attacked by Saturn's gas creatures, a closeup of Superman has his cape as blue instead of red.
When Toyman launches the frozen Superfriends to Saturn, only ten of them seem to be encased in the ice. From that moment until the point where they eventually escaped, Aquaman is nowhere to be found.
When the Superfriends are frozen in the block of ice, notice Hawkman's and Wonder Woman's costumes. His arms and chest are mostly uncovered. Her shoulders, arms, and legs are all uncovered. It's amazing that they don't get frostbite. (editor's note: well, they can both survive in outer space, which is appreciably colder. Although Wonder Woman sometimes needs a little breathing bubble-helmet.)
Why does the Flash have to wait until they are under attack to figure out how to use his superspeed to get them off of Saturn?
How are the SuperFriends breathing on Saturn? We've seen in other episodes that at least Wonder Woman needs a helmet to breathe in space. Later, everyone is floating in space breathing and talking. The narrator claims Green Lantern is generating a protective field but there's no evidence of any kind of green glow, particularly as they're returning to Earth and only he is seen in the green energy field.