While firing the weapon in the kitchen, Nikita clearly finishes the clip (the slide locks open), but in the next shot the slide is forward again. Also the number of rounds she fires with the second clip (before she checks and finds it empty) is less than the number of rounds she fires with the first clip. It is unlikely that Bob (or anyone else) would give her less than a full clip of bullets.
Nikita's leg gunshot wound heals quickly without a scar.
Nikita's shoes change when she dives into the trash chute in the restaurant.
The Mercedes that Nikita and Viktor drive through the wall repairs itself.
When Nikita is pointing the gun at policeman after the shootout in the chemists, the gun alternates from being pressed up against his chin, to being held a distance in front of him.
French cops have a reputation for shooting first and asking questions later, but the first scene (the drug store robbery) is implausible anywhere in the world. When the officers in the patrol car realize that the burglars have weapons, they would secure the perimeter and call for reinforcements - not barge in guns blazing.
Embassy guards wore Hungarian police uniform however the guy in the staircase spoke some Slavic language. (He said "Dobry vecher!" [Good evening] to Nikita.)
When Bob visits to have dinner as 'uncle Bob', he brings champagne. The English subtitles for the DVD release have Marco say that he will put the champagne in the fridge so it doesn't get "cold". In French Marco clearly says "chaud" (warm), and obviously this makes sense, as you wouldn't put something in a fridge to prevent it getting cold. It is unknown whether this error has been corrected.
Nikita leaves the images captured at the embassy behind in the car with Victor.
Bob claims the gun Nikita gets in the restaurant holds 6 rounds, yet with the first clip she fires 8 rounds and the second one holds 7.
When Nikita ambushes Bob with the metal chair, Bob anticipates the stunt by bracing himself, looking away, and closing his eyes before the chair hits him.
When being dragged from the courtroom after being handed a life sentence, Nikita's back is protected by cardboard inserted into the waistband of her pants.
When Nikita is being taken away after her sentencing, she breaks the top of the wooden bench off. However, you can clearly see it has been cut beforehand to help break off easier.
When Nikita is dragged out of the courtroom, her jacket slides up and reveals her wearing a back protector.
The cameraman is reflected in the bathtub when Marie takes a bath after returning from the embassy.
Nikita is told that she can 'choose her own team' for the operation targeting the E European embassy. It is difficult to see how she can do this, since she has been working alone for an extended period of time, since her release from the training centre.