Plot hole: Elise and Samir are in the back seat of Hub's car near a park, and Hub and his partner are standing outside the car. No one else is in the car. They pass notes as they know they are being watched and listened to. Elise and Samir walk away, and Hub and his partner get back into the front seats of the car and drive off. Suddenly a man jumps out of Hub's side of the front of the car and leads the soldiers in a foot chase. But it turns out not to be Hub, but a decoy, so Hub and partner can slip away. But this guy was not in the car before and they've been under surveillance, so this guy couldn't get in the car unseen and the decoy chase wouldn't have worked if he had been seen getting in the car. (01:33:40 - 01:36:15)
Plot hole: The rape scene in the parking lot... there is no one around for THAT long? But wait, once the detectives come in the scene two people are walking in the background with a shopping cart - they must have seen something!
Plot hole: During David Leigh's narrative about Jim's court case, you are shown a number of newspaper headlines concerning the murders. One shows a shot of Locus looking at camera, with the caption 'Did Locus see his killer?' That shot was on the missing film which was found by David Leigh AFTER the murders were forgotten. So how did the paper get the picture?
Plot hole: Jude kills his victims by biting their necks and drinking their blood - the wounds should be quite obvious, yet the coroners don't appear to have noticed them.
Plot hole: Neighbours had called security to complain about loud music and shouting, but no one called to complain about someone running a power saw in a hotel room?
Plot hole: Batman finds at Belson's home a handwritten list of substances needed for a transplant. Why would Belson, a medical authority in the field that knows those things thoroughly, even write a list down? If it's for Freeze to procure him the material, why would it be at his house and not with him, and when did he even have time to be at home to do that, since he has been kidnapped by Freeze when he was driving on the outskirts of Gotham and taken to the oil rig? If he had time to go home, he at least would have changed clothes, he's still in the tuxedo he wore when he was kidnapped the night before.
Plot hole: Mannie gives his boss the money in time minus the amount the homeless man used. What's to say he won't come looking for him later upon discovering the amount gone, see Lola's casino winnings, think his employee ripped him off then kill both of them before taking the money?
Suggested correction: The money that the homeless spent is not that significant. He can make up that amount by himself.
Plot hole: At the end of the film all the police and ambulance vehicles manage to get into the school, but earlier Keri/Laurie smashed the mechanism that opens the gate.
Suggested correction: There's been a series of murders tied to an infamous serial killer... more than likely the police broke down the gate to gain access. (Which can be done in any number of ways: sawing through the locks, having the fire department dismantle it, ramming through it with an armored vehicle, etc.) They're not going to not come in just because there's a gate they can't open. Also, a quick Google search indicates that often, police are given access codes or ways to remotely open gates at certain buildings (schools, senior centers, etc.) in the event of an emergency. So it's entirely possible they also had a way to open the gate without breaking it down.
Plot hole: After the police arrest Roberts he's flagged for a federal warrant, but Lamb and Barrows don't show up to inquire about him until long after the plane crash. Shouldn't they have been there to pick Roberts up at the police station instead of being sent immediately to a federal penitentiary?
Plot hole: Marion rips the paper into pieces and flushes them down the toilet. We see all the paper go into the toilet. Later when Lila lifts the toilet seat, there's one piece conveniently placed under the seat that couldn't have gotten there.
Plot hole: When the gang opens the gate and enter the house, Dog violently headbutts Charles in the face, but immediately afterwards and throughout the rest of the film, there are no cuts, bruises or swellings on Charles' face.