Plot holes: Joe twice declares that he lives by the rules, leave no traces. Yet throughout the movie, he handles his guns and ammo with bare hands--leaving fingerprints and DNA all over them.
Continuity: Joe shoots two men while his girlfriend isn't looking at him. Blood splatters all over his girlfriends back. The next shot of her back has hardly any blood at all.
Continuity: During the final shootout, the gun Joe is using switches between a Glock and a Sig Saur between shots.
Revealing mistakes: The scene following the one where Nicolas Cage leaves the building after he was caught during his last target, shows the crowd running off in panic. The face of one man in that crowd is blurred.
Continuity: When Joe blows Surat's aide by a grenade in the climax scene, we see the body of the man splits in two. Next shot is of the room door exploding due to the grenade blast. Then again we see the man's body splitting in half. The torso flies off over Joe and the limb portion remains in front of him. In the next shot both the torso and limb parts disappear and Joe goes inside the room.
Continuity: When Joe is sighting the Thai politician through his rifle scope, the reticle changes from a varmint reticle with two horizontal crosshairs and a ladder sight for elevation and windage in the bottom of the picture, to a standard Duplex crosshair with windage and elevation marker lines.