In the subway when he confronts Sinestro, Green Lantern's costume is missing the neckpiece and he has partially-bared shoulders (like Superman's neck-area). Typically GL's costume covers his entire neck and indeed does so in the rest of the episode.
When the Flash breaks the Time Barrier he's running up in the sky.
When Bizarro attacks the future city, his cape briefly disappears.
When the Legion of Doom frees the SuperFriends from the tubes, Batman and Superman's tubes were shown next to each other. Earlier in the episode, Hawkman and Green Lantern's tubes were shown to be in between the tubes of Batman and Superman.
When Superman informs the other Superfriends at the Hall of Justice that he is going to the swamp to find the other heroes already there, Green Lantern can be seen among those heroes still at the Hall of Justice, however Green Lantern had already gone to the swamp and have been captured by the Legion of Doom at this point in the episode.
When Green Lantern and Hawkman are pulled underground by the tree branches, Green Lantern speaks with Hawkman's voice when he says "I can't pull free!"
In the shot where the zombies tear a hole in the wall of the Hall of Doom, the background appears to be of an urban street.
Just after Green Lantern and Hawkman find the BatBuggy in the swamp and Sinestro confronts them, Hawkman's wings disappear.
When Black Manta is observing the zombies penetrating the Hall of Doom's defenses on the monitor, his helmet can briefly be seen as dark-colored, instead of its usual light blue.
Aquaman is not shown when the Superfriends were captured and put in those tubes.
Green Lantern's power ring mace works just fine against Sinestro's yellow sword.
Batman and Robin are encased in an energy cube with a fake Black Manta. But when they're brought to Luthor by the gorillas, the Black Manta dummy is missing.
Six of the Legion of Doom members team up to attack Gorilla City after they leave the Hall of Doom in two ATVs. Grodd, Black Manta, and Sinestro are in one and Brainiac, Giganta, and Toyman are in the other. When Sinestro uses his power ring to pass through the city's shield, he's in the ATV with Giganta and Brainiac, with Toyman seen in the other. They then switch back to the original ATV setup when Sinestro uses his power ring to protect the team from the guards' stun rays.
At the beginning of the final scene, Superman's chest insignia is briefly inverted. That is, a yellow "S" in a red shield before it switches to the standard red "S" in the yellow shield.
Just after the enlarged Apache Chief captures Toyman and a couple of gorillas, Black Manta uses a ray beam that neutralizes his powers and encases him in an energy cube. But this sequence is badly done as it looks like Toyman and the gorillas are shrinking with Apache Chief, and then are normal-sized and inside the cube with him.
When the Legion of Doom make their escape, Samurai and Green Lantern, who didn't appear in this episode, are seen in place of Superman and Black Vulcan, who were among the SuperFriends who did.
When the Legion views Wonder Woman vanishing from existence, Robin's "R" insignia is missing.
When Black Vulcan is first seen at the Hall of Justice before the group is taken by the Legion, he's seen in his original costume from The All-New SuperFriends Hour, and then later when Superman, Wonder Woman, and Green Lantern return to existence.
When Lex appears to Hal Jordan just as he is about to be carried off by a beam of energy, he warns Hal to get out of the capsule while he still can. If he thought it was dangerous, though, why would a heroic person like Hal Jordan let Lex enter the beam of light?
The sun of the planet the Legion sends infant Kal-El to is described as a red sun, even though it is clearly white. A white (hotter) sun would make Superman more powerful, not less.