In the scene near the end, where Travis is beating up Barris, Travis had recently grabbed the blade of the knife when Barris tried to stab him. His hand was shown to be very bloody. However, when the red light and the alarm went on and Travis raised his hands to his head, his hand was completely clean and unharmed.
In the toilet room: in the beginning there is no water in the toilet.
After the toilet scene is over, the guards leave the stall but the door, which is clearly visible, is never opened.
When an "inmate" who has diabetic low blood sugars, he correctly says he needs sugar. But later, still with low blood sugar, he says he just needs insulin. That would lower his blood sugar even more resulting in coma or death.
The movie action takes place in 1971. The experiment participant salary is 1000 $/day. In real Stanford Prison Experiment all the participant agreed to receive 15 $/day (roughly equivalent to $94 per day in 2018)
When all the prison guards talk after the first punishment (ten push ups), one of them said about "that guy from Full Metal Jacket". The Stanford experiment took place in 1971 and Full Metal Jacket was made in 1987.
After using the fire extinguishers on the prisoners everyone is covered in white powder as if a powder apparatus had been used. The actual extinguishers used are of the CO2 type which is easily identified by the big "funnel" at the end of the hose and would not leave everyone covered in white powder.
The guards monitor the prisoners using an array of 16x9 flat screen t.v.'s, despite this being set in the early 1970's which had no flat screen television, only CRT cathodes ray.