Plot hole: One of Snape's memories show Lily telling baby Harry to be safe, be strong. That had to have occurred before Voldemort killed Lily. Snape was not in the house until after Lily was killed and Voldemort was gone. Only Lily and Harry should have had that memory, but not Snape.
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: There is no reason for there to be sinks in the bathrooms. The cars may be able to use sinks just as they use toilets, but in the bathrooms they are too small and too inaccessible for any use.
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: The huge explosion that rips through Tara's house isn't very likely. She only left the stove on for a short while, and if there was really a massive concentration of gas as depicted by the explosion, the Agent who fired the shot that triggered it should have collapsed from inhaling so much gas.
Plot hole: When Puss is being sent to prison near the end of the film a shot is shown of Softpaws effortlessly holding a golden egg with one hand. However, back in the giant's castle none of them were able to carry a single egg without help.
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.