When James is waiting for Layla to come out of CIA with the stolen software, he parks his truck on a lower level just next to the entrance. a) There is no such lower level near the CIA Langley entrance (even at a far away distance). b) If you park or mistakenly drive into the area near the entrance, in no time you would see gun trotting cops knocking on your windshield.
When the recruits are playing poker, Clayton sees Zack's raise. Ronnie then folds. At that point, the betting should have stopped, but Zack then bets again and Clayton sees and raises his bet, which causes Zack to fold.
When Burke is telling Clayton about his start in the CIA, he says he is "fresh out of Ocala, Florida", but he mispronounces his hometown "Ocala" as "OH-kuh-luh" when it's actually pronounced "Oh-Cal-Uh".
During the scene where Clayton is kidnapped and put in the "Breaking test" cell, he's seen with his hands at his side and un-cuffed. He even manages to throw his food at the door and punch it before sitting down still cuff-less, however, when the "guards" return to the room, he's lying on the floor with his hands re-cuffed behind his back.
While training at The Farm, the recruits shoot at paper targets. When they are told to "stand and holster" and the targets reeled in, it can be seen that none of the paper targets have any holes in them.
The magazine of the Glock gun with which Clayton threatens Burke has an extension floor plate (which is angled and protrudes down from his hand). When Burke knocks the gun out of Clayton's hands and it lands in the rear of the car, the magazine has a standard (level) floor plate.
Clayton, following a suspect, jumps out of a train which is standing in the station onto the rails on the other side of the platform. A public train will only have its platform doors open, never the doors that give access to the other railway.
In the movie, John Medica was identified as the VP of Dell Engineering. This was correct when the movie was produced (he has since retired from Dell). But Al Pacino pronounces his name as "Me-de-ka". John pronounces his surname as "Med-uh-ka".
When James is entering Layla's secure work area, it sounds as if he enters 5 keys (each strike emits a beep), but only 4 coded (asterisks) marks appear. Many keypads require that either the pound or enter key be pressed after the code is entered. This also makes a beep, but does not cause an asterisk on the screen.
During the intro sequence one of the shots of the James Clayton web site reveals the address bar, exposing that it is in fact just a mock-up designed for the film and is not a web site on the Internet.
During the title sequence of the movie a website is shown where Clayton posts information about his missing father. If you look at the address bar of Opera's browser, it says "file:///vault1/projects/recruit/design/images/sourceimages/fakesite/htmled_site/page_02.html" - clearly a local reference to the "fake" website.
The goof items below may give away important plot points.
Burke tries to convince Clayton he has blanks in the pistol. Clayton checked the magazine when he first received the weapon. He would have seen right away if there were blanks, as they look quite different from real rounds. He had also fired such weapons in the firing range, and this weapon at Zack. Blanks have no recoil so he would have immediately noticed the difference. Burke would know this, and would not have tried such a useless ploy, no matter how desperate.
When Burke emerges from the warehouse in the final scene the slide on his weapon is locked to the rear, signifying an empty magazine, unloaded condition. The weapon then appears with the slide forward, signifying a loaded condition. As Burke turns away, we hear him release the slide catch even though the slide was already released and forward.
At the end of the film, after Pacino's character dies, none of the agents go into the building to retrieve the laptop containing the vital and classified Ice-9 program. Colin Farrel's character and the other CIA boss simply drive away without the laptop.
If there are no printers or disk drives allowed on the classified network, USB drives would also not be available. The whole purpose is to limit or eliminate the ability to exfiltrate material from the network.