When Helen Wicke interrogates Nikita, her bangs are braided. After Helen slaps her, as the cut camera cuts back and forth between the two women, Nikita's bangs are, in some frames, completely undone and, in other frames, braided all over again.
When the bin that is dropped from the sky is first seen, it is a large bottle green container box and is exposed. Later, when Nikita goes to retrieve it, it's become a much smaller black box and is half buried onto the ground.
When Nikita is searching the "guest house" at night, Peta is careless when she turns, and shines the flashlight out the windows. This would have signaled to the outside, and the guards would have been prompt to surround Nikita. Peta should have instead pointed the light to the floor when facing the windows.