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.
Plot hole: During the nova scene, everyone is tying down the sails after securing themselves with lifelines to the mast. Jim and Silver are on the front and Silver is knocked off. Jim is then all dramatic and runs to grab Silver's lifeline which seems to be coming from above, and pulls Silver up like a pulley. How come? The lifelines were attached to the mast, so Jim's action is pointless... even if he could do it, because a shot later both lifelines are streaming right to the mast, leaving no room for a pulley of any sort.
Plot hole: There is no way that 'coast of Iceland' could ever have been mistranslated as 'coast of Ireland'. For this to have happened, they would have had to have thought that the 'C' rune was an 'R' rune, but they had already deciphered the word 'coast', so they knew what the 'C' rune was. The 'O's are the same rune and the 'A's are the same rune, plus there is one rune for every letter, so it it's a direct letter-by-letter translation.
Plot hole: After Little John bores a hole in the bottom of the treasure box, several gold coins fall through the hole. The four rhinos holding the box should have noticed it becoming lighter.
Plot hole: In the scene where the Sheriff stops the cows' brawl, he gives them to the Chinese man. The Sheriff knows what Pearl's animals look like, so why didn't he recognize the cows as Pearl's?
Plot hole: When Sykes chases the gang down the subway, Fagin has to lurch to the left to end up on the subway tracks. However, Sykes couldn't do this because his car is to big to fit. Instead, his car jumps onto the subway tracks as if he were on a platform that separated the tracks, which subway tracks most certainly do not have.