Continuity mistake: When the Wicked Scary Monster first reveals itself in the Titan's Tower, we see the Titans huddled together in chibi-form after the commercial break. At first we see the Titans cowering behind Robin, who is standing in the middle, but when we see the Monster again up front, suddenly Starfire has taken the center and Robin stands between her and Beast Boy.
Continuity mistake: Within the timestream, Starfire rips off Warp's vortex regulator with her left hand. She still has it in her hand when she first shields her face with her left arm, but as we see Warp dropping out of the timestream and Starfire following right afterwards, both of her hands are empty.
Continuity mistake: The animated video shelf which goes after Beast Boy uses red and grey DVD cases as eyes and teeth. When Beast Boy roars at it as a T-Rex, the shelf loses its "eyes" and "teeth" out of fright, but when Beast Boy charges into it, it suddenly has them all back on.
Continuity mistake: After the video rental clerk shoves the Wicked Scary DVD into Beast Boy's face, the scene fades to the evidence room where Robin is depositing Control Freak's remote. In the showcase to the left which holds the masks of Slade's robots, we also see some of the Puppet King's Titan puppets and his soul-switching control, which got crisped in blue fire in first season's "Switch"; therefore it should not be on display. (Switch to slow run to detect it; it's rather difficult to catch on normal speed.).
Other mistake: Beast Boy and Wildebeest fight in a cage suspended in an endless room, with no solid ground underneath. But during the fight both combatants keep stepping onto the gaps formed by the cage bars without their feet falling through, as if the cage bars on the bottom side are merely painted onto a solid surface. For instance, watch Beast Boy's feet when he turns into a skunk.
Continuity mistake: The Titan Communicators' lids depict the Titan's logo: a white T in a black circle, encased by a yellow rim. When Robin calls up the other Titans after recovering from his paralysis, the lid of his com device has a black T in a rimless yellow circle; later it has the standard design described above.
Continuity mistake: After claiming to Cyborg (her last remaining teammate) that she never gets scared, Raven turns away to find him missing; at that point you can see the cellar door in the right-hand wall. But when the winged shadow monster appears and Raven turns to run, the cellar door is gone.
Plot hole: The alternate future Cyborg must stay connected to a large and heavy generator, which stands in the Titan Tower's common room, in order to remain functioning. But as we can later see, the power cables have a rather limited length, and the device is obviously too heavy to move easily. So how comes that Cyborg can roam the Tower and come through the common room's main door, where he appears when he confronts Starfire, without even any of the thick cables showing?
Continuity mistake: Starfire intercepts Soto's ship upon take-off and pushes it back to Earth. But when Soto proceeds to activate the lift-off thrusters, look at the UFO's window: the canopy of treetops moves in a fashion which indicates that the ship is currently moving up, not down.
Continuity mistake: After Robin slides Starfire's cocoon away from the Chrysalis Eater, the monster is attacked by Raven, Cyborg and Beast Boy. As it turns to fight back, we first see the cocoon lying all by itself in the background, and then suddenly Robin pops back into the frame.
Continuity mistake: When Kitten makes Robin lead her onto the ship, Starfire is crush-gritting her teeth, then she slams her fist onto the hood of the car on her right side. When she skids into the picture, the car in question is a red sedan, but when she hits it, it suddenly is Kitten's pink Rolls Royce, which was standing in front of her (and slightly to the left) just moments before.
Plot hole: During and right after Cyborg's, Raven's and Beast Boy's fight against the mutant moths on the bridge, they contact Robin via their communicators. On at least two occasions, when their faces are seen on Robin's com and the main computer screen, the members of the trio appear not to look onto the screen of their own communicators, but at a separately mounted camera somewhere nearby.