Plot hole: Right after the Joker goes into the cathedral with Vicky, Batman follows him with no one else entering in between the two parties. How then did Joker's goons get to the top of the cathedral before Batman or the chopper? They couldn't have planned it since Joker had to tell them where to pick him up, and they didn't know he would chase after Vicky to that particular location.
Plot hole: During Riggs' last fight with Adolph, Adolph holds the knife in his own hand as Riggs forces him to stab himself very slowly. At any point, Adolph could simply have let the knife fall or just tilt down before that happened. Nothing Riggs is doing is making such impossible. "Locking" his wrist does not prevent him from letting go of the knife. It only prevents him flexing his wrist. And this guy is a trained killer, fighting for his life. Better to battle for control of the knife than just let it kill you.
Plot hole: Bond goes after Lupe after she leaves the casino table, and they have quite a lengthy, hush-hush conversation. It's a casino, and there are cameras everywhere. Certainly, this would have been brought to Sanchez's attention since he was already leery of Bond and possibly Lupe.
Plot hole: David Sutton claims he's never read an autopsy report before yet earlier he said he moved to his new town to get away from all the murders he investigated, a job that would have required him to read autopsy reports.
Plot hole: Megan is suspended because the police were not able to find the gun the robber had (stolen from Eugene at the scene) and believed that she had killed an unarmed man. This is very unrealistic because surely they would have interviewed all of the hostages/witnesses at the robbery and each would have easily confirmed that the robber had a gun, and possibly that Eugene might have been missing right after the incident.
Plot hole: Given the store's being bought by a retail chain like Kroger's there's no reason Bill's partner can't sell him his share in it, get half the price they're receiving for it then have Bill make quarterly payments to him. They could've also got the new owners to keep Bill on as manager as well as keep their employees or void the sale.