Teen Titans (2003)

Kole - S5-E6

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.

Titans Together - S5-E12

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.

Titans Together - S5-E12

Plot hole: Speedy's bow got cut up by Cheshire in the previous episode ("Calling All Titans"), and in the Brotherhood base he is seen frozen with empty hands raised. But when he is unfrozen in this episode (zoom in to check), he suddenly does hold a new bow in his hands.