Darkness and Light: Part 1 - S1-E11
Plot hole: When Hulk and Banner have been physically separated by the nutrient bath, they are both wearing tattered pants. Given that Hulk and Banner were previously occupying the same body, this should not be possible. Hulk was the one that went into the nutrient bath, so if Banner's body was separated from Hulk, then Banner should be naked.
Suggested correction: It was done deliberately as a form of censorship. They didn't want to show Bruce's genitals.
Explaining why the mistake occurred doesn't invalidate it. Unless you're suggesting the nutrient bath also was able to duplicate the pants.
You realise a character can be drawn naked without actually showing their genitals (and/or breasts in the case of women), right? The Little Mermaid is a good example of this.
Plot hole: Series 2, Episode 11, The Agenda (1). The Tripredacus Council explains that Ravage will be able to find Megatron and the others by tracing the transwarp wavefront back through time to its source. If he truly did follow it back to when it started he would have arrived moments after Optimus destroyed the alien weapon in "Other Voices: Part Two" which created it, yet he arrives considerably farther in the future.
'Unmei no sentaku' mitaina - S1-E6
Plot hole: Akito's attack is point blank, on a ship part of a fleet with Distortion Field activated (basically, they have shields, like the good guys' robots). The explosion he causes is according to Ruri's damage report big enough that it managed to vaporize 80% of the ships they were facing, but his Aestivalis and the other 3 right floating nearby make out of it literally without a scratch. (00:05:10)