Continuity mistake: Robin is chasing Red X. Red X throws a net of some kind onto Robin, then Robin says, "I'm fine. Get X. Go." and points toward Red X. Later, we find out that this was actually a hologram of Robin, when Starfire accidentally activates it again. However, this time, the hologram of Robin does not point after his dialogue.
Continuity mistake: After Cyborg switches the microphones back on and Raven asks whether he could 'accidentally' leave it off, Beast Boy swells his vein. In that shot you can see the yellow marking stripe from the Titan Tower's sub hangar outside BB's canopy, however, at this time they are already in the deep sea. It's simply a repetition of an earlier scene.
Continuity mistake: When Beast Boy and Aqualad each spot one of the Trident clones in the volcanic cave, they look away from each other, but when they try to point him out to the other, shouting "There he goes!", they are pointing over to the direction opposite the one each of them was just facing.