When the warden has been locked in the prison and the prisoners are charging at him, the shot facing the guards when they open fire on the prisoners clearly shows the warden climbing the bars, then cuts to a reaction shot of the warden still stood normally on the floor, then shows another shot of him climbing the bars.
When Scagnetti is with the prostitute, as he starts to choke her and they roll off the bed, he is seen wearing a thong with just a string in back. When he gets up and is seen standing by the window, his underwear has changed into briefs.
Leading up to the Super Bowl the number of victims that Mickey and Mallory murder change several times from fifty six to fifty seven to forty eight and other numbers in the deleted scenes and unrated cut. This might have been done deliberately by the film makers to give the killers the larger than life pop lore they wanted.
Several times during the Prison riot scenes people's weapons constantly reload 'magically' as no one (save Mickey) is ever seen to be reloading their weapons, nor even seen to be procuring shells or magazines from the bodies of guards, yet they still continue to fire. Again, this comes from reading the film too literally; the riot is not supposed to be taken as a realistic depiction of a riot.
During the prison riots, guards can be seen firing from a security tower with their shotguns, only to have several prisoners overrun the tower. This makes little sense as all guard towers have doors with locks on the inside. Again however, this is coming from reading the film in too factual a manner. The riot is not supposed to be a realistic depiction of such an event.
During the Prison Riot all the doors seem to be magically opened, the reason supposedly that the doors are jammed. The security locks in prisons are tested several times a day, and at the beginning of a riot all the doors would close and lock. However, as with the issue of the snake bites, this comes from an overly literal interpretation of the film, something which Oliver Stone strongly discourages on his DVD commentary track. The riot is not meant to be taken as a realistic depiction of an actual prison riot, and Stone acknowledges that great liberties were taken in the scene with the full knowledge that they weren't realistically accurate.
No-one would be physically or mentally capable of casually walking around a shop after being bitten by a rattlesnake. However, as director Oliver Stone points out on his DVD commentary track, the snakebites are not supposed to be taken literally, but as a metaphoric infusion of 'knowledge' from the Indian shaman. He acknowledges that in reality, they should be dead, but he argues that the film is not a realistic depiction of reality.
No human can take such a repeated and concentrated dose of Mace as Mallory does and open their eyes so soon afterward, not to mention Mallory's eyes open quite easily and do not shut during the spray. Mallory also doesn't apply any water to her eyes, and seems to recover naturally only minutes later. This is one of many scenes which are supposed to be stylized and unrealistic.
When Mallory attacks Scagnetti in her cell and the guards rush to unlock it, you can clearly see it is at the end of a hallway (one guard pushes the other one out of the way as they both scramble to unlock it. But when Mickey reaches Mallory's 'cell' to rescue her, he enters two doors before where hers would be.
It's obvious that the "Drug Zone" is really just a department store, despite trying to be a medicine supermarket. When Mickey and Mallory are wandering through the aisles at Drug Zone, cleaners and other household products are seen on the shelves.
The goof item below may give away important plot points.
When Scagnetti is with Pinky the prostitute, she briefly looks over a magazine on a desk in the motel room. The cover photo is of Mickey Knox, smiling, from the deleted scene of his trial, which is not until later in the film.