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: While the wedding party is getting ready to leave Charlotte's apartment, Big calls Carrie's cell phone. Lily (Charlotte's young daughter) answers, immediately closes it without speaking, then drops the phone into her purse that she takes with her to the wedding. Big continually calls back, but even though Lily is always with one of her parents, no can hear Carrie's phone is ringing inside Lily's purse. Lily only closed the phone, it was not turned off, the ringer was turned up, and the battery was charged. Lily and Harry rode to the library separately and during the time Big had been trying to call Carrie. Harry should have heard the phone.
Plot hole: When Finnegan is in the water and the explosive charges go off, Finnegan should be dead from concussion, and the explosives are big enough to have caused his death by them flinging him quite high out of the water. What happened to Finnegan was pure fantasy.
Plot hole: There is a problem with the warehouse being destroyed to the total surprise of the crew. A building of that size that is bound to be destroyed has to be fenced off days before the destruction, so that no homeless people or kids can easily get on the properties. In this case, however, there was not even a warning sign.
Plot hole: In the scene where Speedman and Lazarus are discussing their acting and Lazarus tells him to never go full retard. It shows these two leading the group, however they stop and talk for quite a while, and the rest of the group are nowhere to be seen until Speedman and Lazarus start moving again. The group finally caught up with them. If at this time, Speedman was still leading the way with the map, how could the group even find these two after being left behind enough distance that this conversation could take place?
Plot hole: At the wine mixer, where Dale is working as a chef , there is a band playing on stage. The drum kit used is the exact same drum kit (chimes and all) as Dale's, as seen in the house. If a band was hired to play they would have certainly brought their own equipment, and there is no way Dale would have brought his personal kit to the event, for somebody else to play. Dale ends up playing this drum kit anyway, when the band walks off and Brennan sings.
Plot hole: Ami's arm was sliced off, and the wound went untreated (you can tell it was not cauterized in later scenes) for a number of hours before it was stitched up. All this time, we see her loosing ludicrous amounts of blood. Yet, Miki looses her foot, and dies of blood loss only a few minutes later, despite her wound and blood loss being much less severe than Ami's. An inconsistency in the style done solely for dramatic purposes.