Plot hole: At the start of the movie, a great deal is made of the boom mic that enters the shot. This is ridiculous, because Bolt's view would not be restricted to what was onscreen, he'd have a perfect view of the person holding the boom mic (as evidenced by it not being stable). There's no possibility of him not seeing the person holding the mic either. As Bolt completely and utterly believes the world he lives in, and thinks the situations he finds himself in (saving Penny) are real, someone holding a boom mic would break the illusion for him. In all instances in the movie where an outside force (i.e. a dog handler) interacts with him, Bolt never gets to see the person handling him (handler approaches from behind), the boom mic operator however is literally right in front of him.
Suggested correction: He wasn't paying attention and considering that his focus was only on the "action", how the hell would he notice a boom mic when he's trying to protect Penny? His "reality" is never broken even AFTER he's in his trailer.
Plot hole: The newspaper headline showing young Alex being rescued from a crate is dated April 8, 1972. In the next scene, we see young Alex dancing in the Central Park Zoo, and watching him are Marty, Melman and Gloria as baby animals. This makes no sense at all. In the first film, Marty celebrates his tenth birthday. Key word: tenth. It is also known that the scenes of the main characters as adults take place in the present i.e. Alex confessing to breaking Marty's iPod. Seeing how the animals age quicker than humans, Marty, let alone his three friends, would have to have been born in the mid-1990s and the flashback scenes could not have taken place in 1972.
Plot hole: When Tinkerbell tries to find Gruff in winter, she's seen flying with her wings out of her coat; in a later scene, Fawn flies too. After Tink finds Gruff, her wings disappear from underneath her coat. This is a plothole because of how the whole storyline of Secret of the Wings was that warm fairies can't fly in winter weather or their wings will tear.
Suggested correction: Yeah but at the end of Secret of the Wings, they find a way to let any fairy fly in winter.