When IDAK attempts to "Crush, kill, destroy" the alien hiding in the Jupiter 2, Will runs over to stop him. When Will's father goes to stop him, he has a rifle in his right hand & grabs Will's shoulder with his left. When the camera angle changes, his hands have switched -- the rifle is suddenly in Professor Robinson's left hand, and he's grabbing Will's shoulder with his right hand.
After IDAK pounds on the door of the Jupiter 2 with a boulder there is now obvious dents and scarring. When the door is seen later it is once again smooth and pristine.
When Dr. Smith is training with IDAK an obvious stunt double is used. The double has darker hair as well as differently styled.
When Dr Smith is training IDAK in hand-to-hand combat, IDAK punches Dr Smith in the forehead. When Dr Smith falls to the ground, his elbow and head land off the silver mat, but in the next camera shot, his head is landing in the middle of the mat.
Dr. Smith claims to be the "supreme brain of the universe" but moments later doesn't know how to spell IDAK's name. IDAK is prominently displayed in large letters on the breastplate of his uniform.
Will shows the first IDAK a softball but refers to it as a baseball.
At about 30 minutes, the official voice giving Omega 17 his instructions says, "You will destroy anything, including humans, that get in the way of your target." This should be "gets" because anything is singular and the additional phrase does not make it plural.