Continuity mistake: During the first 20 minutes of the movie, Patricia is wearing a pearl necklace. When she is shown sitting in the car, it is a double string of pearls. After she has crashed the car and climbs out, it is a single string of pearls. When she and Joe are running through the jungle, it is once again a double string, and when she returns home it is a single string again. This can not be explained by the necklace being a long string of pearls that's draped twice around her neck, as the necklace is always shown to reach just below her throat, and a longer string would reach further down.
Continuity mistake: Near the end of the film when the black star ninja and the yank ninja are fighting, they come to a wall with rope hanging down and start to climb.When the camera switches back and forth, you can see that they have both chosen the same rope (they both climb on the rope marked "Gin") even though they are side by side when they climb.
Revealing mistake: During the Army assault on Ortega's compound, Jackson is shown as he uses a machine gun to clear a long balcony of enemies. The third person he kills here is hit several times, but does not fall over the railing. Instead he slowly and carefully climbs over it, lifting one leg over at a time.
Plot hole: When Dudikoff gets Ninja training from the old gardener before his final confrontation with Black Star Ninja, the gardener says "The time has come for your final lesson" and then introduces him to the throwing star and the ninja sword. If this is the final lesson and he's only being introduced to these weapons now, how come Dudikoff used these weapons successfully earlier, against about 15 ninjas in the fight at the warehouse trap?