Deliberate mistake: Cyborg, Starfire, Raven and Beast Boy are kicked out of the Tower by the HIVE, and the trio watches them from the Operations/Main Living room panorama window. But whenever Jinx, Gizmo and Mammoth are seen (before they send in the tidal wave), the same window is on their right-hand side, whereas there should be a solid wall separating Ops from the side wings.
Character mistake: When the Puppet King first prepares to incinerate the Titans, Starfire (in Raven's body) and Raven (in Starfire's body) watch from a catwalk above. We can hear Starfire gasp and Raven say "No"; but curiously they do so as if they were in their respective actual bodies (i.e. Starfire's body gasps and Raven's body says "No"), whereas for most of this episode each of the girls talk with her own voice in the wrong body.
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.
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.
Other mistake: When the probes are going off in the Titans, including Robin, Slade rips off his arm piece that houses the red button. When he does this, the probes stop. However, it would have required clicking the button again rather than just breaking it off the rest of his suit. (00:19:45)