After the evil ninja comes out of the lake he is soaked from head to toe. In the next shot, he continues to fight police officers and is bone dry.
When Christie throws a ninja star at Officer Case she is on one side of the pool table close to him. When he then throws a pool ball at her, she is suddenly on the other side of the pool table further away.
When Billy confronts Christie as she steps out of the shower (after the massacre at the cemetery) she has a huge ugly bruise over her right eye. She attacks Billy and leaves, going to the old temple. She gets there, fights the good ninja and passes out. When Billy finds her and pulls off the ninja hood, the huge bruise is gone, all in the shade of about an hour.
In the helicopter, the Black Ninja kicks the pilot unconscious, but leaves him in the helicopter. The cop behind him says, "Hold on, I'll go and get him." In the next shot, the pilot has disappeared.
Holes created by the Ninja stabbing through police car roof.
In the scene where Christie crushes a pool ball, it's obvious that the ball is a shell filled with white powder and not a solid ball.
At the golf course when the evil ninja is climbing the tree, one scene he is using a length of cloth to climb and the next the cloth disappears. The next shot shows the cloth is back.
At approximately 1:09:43, When Sho Kosugi is going up a flight of stairs, you can see the plywood wiggling before it falls onto him. Possibly the stunt people reading it for the scene.
After slaying the 3 people at the sauna, Chris and the police officer are talking in her apartment. At 45:45, you see some sunglasses fall from off camera onto her bed.