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.
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?
Plot hole: In Episode 2, "X" and Episode 5, "Haunted" we can see the mutant larva Silkie roaming around in the Titans' Tower. But Silkie is officially introduced to the series in episode 10, "Can I Keep Him?" - so how can he just appear in the TT's commando center without raising even one curious eyebrow to his thereto unexplained presence?
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.
Plot hole: When Beast Boy finally brings himself to disable the Destruct-O-Tron, the hole he punches into the device to get inside is already visible when he is still bracing himself for the plunge. This background was simply reused for the scene where the device shuts down for good.
Plot hole: When Beast Boy hires at Meaty Meat, he takes away the ad "Human Help Wanted" from the window right next to the door, and when the Titans come by for a meal later on, the sign remains gone. But as the Nufu ship reveals itself and the restaurant clients panic, the sign is suddenly back in the same corner of the window, even though it is unlikely that the Nufu Source/Bob would take in more hired help and risk being discovered all too soon.
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.
Plot hole: After the Titans have recovered their senses, they engage Mae-Eye and her gingerbread men. Just before Cyborg and Raven are trapped in giant jars, they blast Mother Mae-Eye directly from behind. But for her to enchant them, she just turns to her left and casts her spell to her side instead of behind her.