Plot hole: If the government guys could see Daryl in the cockpit, they should have known they could finish him off. If they launched a missile, he would either be hit by it or cook himself himself trying to outrun or outclimb it.
Plot hole: In the first Jungle Book movie, the role of the vultures is that they do not seem to be hesitant when helping the boy, Mowgli in need of help from Shere Khan. However, in this movie, when their obnoxious vulture friend is attacked by Shere Khan, they do absolutely nothing to help him and in fact, fly away cowardly. Did they suddenly lose all of their courage?
Plot hole: Buddy discovers a website, myearth.sat. The site, like Google Earth, contains satellite images of every square inch of the planet. Buddy can see his neighbor's house but not his own house. He decides to cover his house with lights so it can be "seen from space." There is absolutely no reason why the site would show every house in the world except Buddy's, except that the oversight is required in order to advance the plot.
Plot hole: How did Dolittle manage to rescue an incredibly heavy bear from drowning? He must be unbelievably strong to be able to drag a bear of that weight. (00:35:25)
Plot hole: In the scene at the little girl's party where Cat is the pinata, and he gets whacked in the groin, he screams out loud, all the kids hear him, you even see their shocked faces as well. But after Conrad and Sally throw the lollies, the kids totally forget about Cat yelling - hardly likely given the level of shock. As well as that, wouldn't the kids have noticed that the Cat didn't have a hole in it when they saw the lollies? They just came from behind a bush. And to top it all off, in the scene where all the kids are greedily on the ground grabbing the lollies, and the Cat's about to hit the kid that whacked him, in the bottom left corner, a little girl looks directly at the Cat, Conrad and Sally.
Plot hole: Major plot leak: How could Flint's ship get into the lake atop a tall volcano all in one piece? If he wanted to merely hide the treasure in order to recover it later, the whole setup, including the lake's draining system, would be totally unnecessary, and it looks all too deliberate for the ship to be sitting in the lake by accident (say, thrown in by a violent storm).
Plot hole: When the 3 ninjas' Grandpa is in hospital, he phones them and complains that no-one at the hospital speaks English. Not only is this a strange complaint to make about a hospital in Japan, but later in the film he is seen speaking in Japanese. He should therefore be able to easily communicate with people at the hospital.
Plot hole: Kahuna seems to be about five or six, yet the formula he took stopped him from aging, even though he was a baby when he took it.
Plot hole: After the secret passage has collapsed, the Black Fox hires Hawkin's midget acrobat friends because the only opening left "is barely (wide) enough for a child". Yet, during the throne room brawl, Hawkins passes the swing-around rope to a guy who is much taller than the midgets.
Plot hole: In the scene before Maya rides in the barrel race, They emphasise that Brooklyn has broken her hand, thus making it necessary for Maya to ride without any prior training, yet after they have won, and they are all jumping around for joy. Brooklyn's hand is not bandaged and she would be in an enormous amount of pain waving her hand around. Also at Mayas birthday party, Brooklyn has not bandage and is waving her hand around like there is nothing wrong with it.
Plot hole: When her father is taking the "shortcut" he somehow doesn't need to shift gears even though he has a manual transmission. At the speed he was at he should be in at least 2nd gear.
Plot hole: Vanessa seems upset at Barry when their actions at getting the honey back from the humans result in the flowers and other plants dying. One might think that Vanessa, as a florist, would know the outcome and would warn Barry instead of helping him with his plan. Yet she appears to blame him for the entire outcome when it becomes apparent.
Plot hole: When Grug is trying to escape from the explosion behind him he sees Douglas and says "Douglas! Hey I know that guy!" This is not possible since he neither knew the name of the creature or was nowhere around when Douglas was with Thunk.
Suggested correction: Thunk might have told him who Douglas is.