Plot hole: After the battle, when Robin tosses Beast Boy the Brain for freezing, the Puppet King is seen among the assembled Titans (on the right, next to Herald and Jericho). Somewhat odd, considering that the Puppet King is a villain and not getting frozen up like his compatriots.
Other mistake: Among the Titans groaning over Beast Boy's "brainfreeze" joke, we see XL Terrestrial, the pale-turquoise alien-looking guy with two antennae who can grow to large size. Again a mix-up of hero and villain identities, since XL was in the H.I.V.E. and the Brotherhood of Evil and should therefore not be among the young heroes. You will also see the Puppet King by Jericho.
Other mistake: When Red Star introduces himself, he takes off his parka with both hands. But as it drops to the ground, you can see the fingertips of his hands on top of the screen, standing completely still. This setup looks unnatural, as if he had suddenly taken off the parka with some telekinetic power.
Continuity mistake: When Kid Flash and Jinx arrive to give a helping hand, the remaining H.I.V.E. Fivers stare at her, aghast about seeing her on the heroes' side; Billy Numerous even points at her. Before (when Cyborg is slammed into the stairs) and after (when Kid Flash races off into the fray) that particular shot, however, the H.I.V.E. Fivers' stances and expressions just remain the same.
Continuity mistake: When the HIVE Five corner Kid Flash in the museum, See-More activates his laser eye, which is red. But one cut later, when Jinx walks up saying "you're a little slow", his eye has its standard vision coloring again. And before the commercial break See-More puts his left hand to the visor switch, but after that he has his right hand up.
Continuity mistake: In the shot immediately after Beast Boy says "Uh guys, I think they're know we're here", where the lizard men are entering the scene, Starfire is in her normal sleeveless outfit. In the shot immediately before and after this, she's wearing a full suit of Tamaranian armour. (00:18:05)
Continuity mistake: Más y Menos figure out how to use Professor Chang's Cryogenic Machine to unfreeze their fellow Titans and do the reverse with the opposition. But the few times where they are seen actually activating the Freeze option - Professor Chang and his assistants, and later the HIVE Five -, they push a different button in each instance.
Plot hole: When the raptors bring down Beast Boy in his Tyrannosaurus form, he escapes the batch lying atop of him by turning into a dragonfly. When he does so, the heap of dinosaur bodies does not sag down at all, and to fill out the gaps, a whole lot of additional raptors appear in his stead from God-knows-where.
Continuity mistake: When Kid Flash intercepts Gizmo's shop-lifting, Gizmo was walking towards the exit with his shopping cart. But after Kid Flash has deposited Gizmo in the cart, he pushes it on towards what would be the back of the shop, away from the entrance. But then Gizmo bursts out of the entrance into the parking lot beyond.
Continuity mistake: When Raven is ambushed by Kyd Wykkyd and Psimon, she looks at Psimon over her right shoulder (since Kyd Wykkyd sits on the canopy in front of her). But when we see the outside of the pod, Psimon hovers in the air to the left side of the pod; he even casts a glance over his right-hand shoulder, i.e. to Raven's own left side, while she keeps looking to the right.