Continuity mistake: The blue paint blob on the painting changes between shots. (00:47:00)
Other mistake: When Tom is being hit with the fruit, he is being hit high enough for Bee to see the fruit but doesn't react to random fruit hitting Tom. (01:00:15)
Factual error: The rabbits are underneath the landrover, and they get shot out the back whilst holding on to the axle. Land rovers have an enclosed axle with a hub enclosing the diff, so this would not be possible.
Continuity mistake: Tom grabs some explosives out of the burrow, and as he stands up some have appeared in his pockets.
Revealing mistake: Cottontail gives Tom a wet Willie. However Tom reacts before Cottontail touches him.
Continuity mistake: When Mr McGregor collapses, his hand goes from open to closed, depending on the angle. His position in relation to the carrots keeps changing too. (00:11:40)
Continuity mistake: Tom McGregor puts all the gates up and closes them, however when Bea arrives the gate is open.
Other mistake: When Tom is choking Peter, for a moment, Peter disappears.
Factual error: Thomas McGregor asks at the station in London for a 'round trip' ticket to Windermere. It's called a 'return' in Britain and no British person would ask for anything else.
Other mistake: When we see the 4x4 driving to the hardware store the truck isn't reflected in the shop windows even though it should be.
Other mistake: On the way to the river the rabbits can pull the tail gate up from inside the back of the 4x4 and it closes and stays shut. However in the shop, Tom is shown that a clip on the outside of the 4x4 has to be bolted to keep it shut.
Continuity mistake: When Mr McGregor has died, all the animals run into his garden and Ms. Tiggywiggle is at the very back. When we see the gate being broken down a second later she is at the front.
Continuity mistake: When they climb the tree at the start the positions of the rabbits change instantly.
Continuity mistake: When Tom uses the binoculars for the first time the strap is draped over his arm. Camera cuts and it isn't.
Continuity mistake: Benjamin gets trapped with his jacket being pierced and pinned to the gate. However when he puts the jacket back on there are no holes.
Other mistake: The postman delivers a Royal Mail Tracked 24 hour envelope to Tom and asks for a signature. However the label on the letter states no signature.
Continuity mistake: The land rover's position at the hardware store changes between shots. Note the yellow line.
Continuity mistake: When McGregor collapses his glasses come off and end up on the lenses. Camera changes and they are flat on the floor.
Continuity mistake: At one point when Tom is chasing Peter and Benjamin for the first time, he hits the ground with a tool, camera turns 90° to the left and now Tom is in front of the camera again. No way for him to cover that distance instantly.
Continuity mistake: When the rabbits are watching Tom clean the greenhouse, Bea mentions McGregor, at which point Cottontail pulls out a blackberry and squashes it. In the next shot the blackberry is gone and Cottontail's paw is completely clean.
Answer: It's not clear if he actually can hear them or not. It's implied in the film that it's possibly stress or a mental break that is causing him to hallucinate their voices, or is suddenly thinking on a brain wave length that can understand them. If it's the former, it's coincidence that he hears similar to what Peter is actually saying. Either case explains why he suddenly can hear them when nobody else can around them despite them talking in front of people.
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