Continuity mistake: During the Sword fight scene, 47 pulls a katana out of a dead agent's hand, in order to use it. It is covered and dripping with blood. However when he comes to use it a few seconds later, it is clean as can be.
Continuity mistake: In the scene in Africa, after the prisoner has his arm chopped off, when the warlord pulls out the cloth gag from the prisoner's mouth and asks another man about the prisoner's voice, the gag is back in place.
Continuity mistake: In the railway station where 47 is being followed by the FSB, Interpol and the older agent, you see the older agent running down the ramp to platform 9 after 47. His jacket is flying up in the back, and there is no weapon visible. When he stops running, he reaches behind him into the waistband and produces a handgun with a silencer.
Other mistake: The FSB uniformed guards in tactical gear have stencils on the back that are lettered incorrectly. The Cyrillic F and B are correct, but the Cyrillic S looks like a C not a backwards C as shown in the movie.
Continuity mistake: When the helicopter gunship shoots through the window of the cathedral's tower, bullets are seen to pass through Belicoff, leaving his chest in the direction he is facing. However, when the camera angle changes, the helicopter is to his side, at 90 degrees from the shooting in the previous shot.
Deliberate mistake: A stunt double for 47 got hurt on camera and yelled, very obviously. Right after the sword fight on the train the last man 47 is fighting continues the fight hand to hand under the tracks. Timothy Olyphants stunt double throws a punch and he grips his hand, yells and his face comes into screen for a moment. Next shot, Timothy Olyphant throwing his own punches.
Factual error: At the scene in the church, there are lots of security personnel standing around wearing steel helmets. The helmet type seems to be an East German M56 helmet (standard for the East German Armed forces until reunification). There is no reason why a Russian security force would have the M56 helmet. (Only if the makers of the movie where able to purchase a lot cheaply :).)
Factual error: When 47 shoots the two soldiers in the hotel, they die instantly. In reality, a person shot with only one bullet still has about 1-2 minutes of normal body functions before they lose consciousness - it is not unknown for people to fail to realise that they have been shot. (Police trainers often report that their students are surprised when their targets aren't killed at once but instead get back up and retaliate). The soldiers wouldn't have been taken out instantly and should have had more than enough time to fight back. And they were wearing body armour, which should have been enough to stop a pistol bullet from causing an instant kill.
Continuity mistake: Near the end, in the church tower, after the inspector arrests 47 and he is escorted by the soldiers from the tower room to the van outside, the inspector remains in the tower room while the soldiers, together with 47, leave. Next, we see 47 and the soldiers walk down the steps of the church building and head to the waiting vehicle - and the inspector is already there waiting for them. He couldn't have beaten the soldiers to the car; they left first.
Plot hole: In the scene where 47 swings out of the hotel window, we see the booby trap starting to explode as he's still in the room. Then in the shot from outside, the explosion extends out the window - so how on Earth did he outrun it and get out completely unscathed?
Continuity mistake: When Agent 47 snipes Belicoff soon after the beginning of the film, he shoots the guard to Belicoff's left first, to allow a clean shot at the president himself. However, when the camera zooms to 47, you can see that he is directly in front of Belicoff, not to his side, so he needn't have shot the guard first; he already had a clean shot, and shooting the guard first only served to break his cover.