Plot hole: Ham Tyler doesn't recognise Kyle Bates even though he met him in the internment camp in episode 3. Ham also makes exactly the same remark about Nathan Bates in both episodes. (00:10:30)
Desertion of the Dinobots (1) - S2-E19
Plot hole: Perceptor discovers that the reason for their malfunctioning is because their Cybertonium has deteriorated after millions of years of being exposed to Earth's atmosphere. The key word here being 'millions'. This explains why the original Transformers who crash landed on Earth (4 million years ago) are affected, but newer characters like Perceptor, Powerglide, Hoist, etc. are affected despite the fact that they have only been on Earth recently.
The White Mountains: November, 2089 AD - S1-E13
Plot hole: The main characters are being pursued by Tripods, mind controlling alien machines. My question is, if the Tripods can turn humans into 1600's puppets, complete with foxhunts, why don't they make some of said mind-controlled humans help with the pursuit?