Plot hole: When we see Sentinel Prime being extracted from the Ark by Optimus, we can see that Sentinel Prime already looks the same way as he does throughout the rest of the movie. The Ark crash landed in the 1960's, the Rosenbauer Panther Fire Truck didn't exist in the form we see Sentinel Prime transform into. All of the other Autobots came to Earth in their proto forms and adopted a disguise when they arrived [we see them scanning alternate modes - one Decepticon is shown doing likewise in this movie.]. Sentinel Prime already has his disguise when on the ark, which isn't possible.
Plot hole: In the first part of the movie, when the crime boss shakes down the club owner, he leaves a briefcase bomb inside the office. When he walks outside to explode it, the first thing that explodes are the club's billboard matinee lights, nowhere near the office, then the club explodes outward as it should from a bomb.
Plot hole: Everybody jumps into the water and emerges on the submarine except for Natalie. They're wondering where she is when they notice a flare. They realise it's her, and they send a search party. She's hiding on a bus maybe one to two kilometres away from the water. Her going there makes no plausible sense. Makes no sense how she held her breath underwater longer than anybody that they didn't see her and why she would go in the opposite direction of the sub. It was done to prolong the scene. (01:09:00 - 01:18:00)
Plot hole: When Cateleya is in prison she changes into a black cat suit. Where has that come from? Where had she hidden that? She is wearing a very skimpy dress and would not be allowed a handbag or anything.
Plot hole: How did the wolves get across the canyon? Unless they were flying wolves, there's no way they could.
Suggested correction: Just because we don't see how they got across doesn't make it a plot hole. We see next to nothing of the area surrounding the canyon. There could have been a pass or trail in the distance that the wolves used. The characters think they are gradually walking away from where the wolves' den is, so they decide to use a makeshift zipline to get to the other side rather than go back the way they came and risk running into the wolves again.
