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.
Factual error: Near the beginning of the film, Calico is sitting with a cat on his right shoulder. Their reflection is shown in the glasses of a man directly opposite. The reflection shows Calico and the cat in the same position instead of being reversed, as a reflection would be. (00:04:30)
Deliberate mistake: When Penny is loaded onto the ambulance at the end, her gurney is rolled straight in. This is wrong, the paramedics will collapse the wheels and slide the gurney into locks to hold it still during the drive. It was done this way since Mittens and Rhino were hiding in the collapsible section.
Continuity mistake: At the beginning, when Penny and Bolt are acting out the chase scene on the playback monitor, the producers are enraged over a boom mic showing up in the shot. Yet seconds earlier during the actual scene, you don't see the boom mic in the upper right corner. (00:10:10 - 00:11:50)
Continuity mistake: When Penny and Bolt are doing their show at the beginning, Penny is on her scooter when she tells Bolt to "speak" and also when the shot comes up when the camera is right in front of Bolt's face(right before the superbark). But when cam 5 comes up where the man is talking to Mindy Parker about Bolt the scooter is laying on the ground and Penny is not on it.
Continuity mistake: Penny takes a photo of herself with Bolt after Bolt has 'rescued' her again at the very beginning with a Polaroid camera. She places it (the camera) on a counter next to the trailer's door and it is parallel to the edge. Later, after the two cats have taunted Bolt and the camera pans down, the camera has moved and is now positioned at an angle on the counter.
Continuity mistake: The dog catcher looks down at his gas gauge and sees that it's empty, and it's bright daylight. Then in the next shot he's pulling into a gas station and it's night time. Either bad continuity or if nothing else he managed to keep driving until night time on an empty tank.