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: When Charlotte kissed Naveen at the end, she should've turned into a frog as well because she was no longer a princess.
Suggested correction: When ordinary people kiss a frog, they don't transform into anything. (Perhaps they die from infection after a few days.) Charlotte was just an ordinary person. Tiana was chosen. She wished upon the star. Naveen and the consequences of kissing Naveen were a result of Tiana's wish.
Suggested correction: How? She was no longer a princess.
Tiana turned into a frog because she kissed Naveen without being a princess, so Charlotte should have, too.
Plot hole: When Moana first meets Muai, she opens her necklace to tell him he will restore the heart. Muai sees the heart but doesn't get scared until he sees it again on the boat. He should have been scared the first time.
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: Kerchak is mad with Tarzan because he showed Jane, Porter and Clayton to the gorilla's current location. Yet he does not move the group even though he obviously knows they're no longer safe there.
Suggested correction: He does actually move the group later on in the movie. Then they get ambushed by the hunters and he is killed.
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 Wilbur and Lewis are time traveling for the first time, Lewis says he's done with the memory scanner. Since he said he wouldn't invent Dor-15, and she went away, wouldn't the time machine and everything else in the future go away since the memory scanner started it all and Lewis decided to quit?
Suggested correction: Lewis wasn't fully giving up. He was just frustrated and probably went back to it later anyway. Whereas with Doris, he deliberately decided not to invent her because of the danger she posed.
Plot hole: Close to the end of the movie when Sykes is chasing Fagin on the train tracks Jenny says Fagin's name. Fagin also seems to know Jenny's name as well because he says her name and tells her to jump. How did they know each other's names?
Plot hole: Even if Chicken Little was tagged out when he hit home plate, the game was already tied so his team would still have a chance to win the pennant.