When the aliens return to their home planet in the Jupiter 2 after the trip to Earth, the Space Pod is seen outside of the building even though the aliens had docked the Pod earlier.
The hands of the duplicate Robinsons change from webbed fingers to normal and back again.
When the alien first exits the Jupiter 2 the painted backdrop of the standard alien planet can be seen through the doorway, but they supposed to be sitting on a landing pad in an industrial location.
During takeoffs and landings the circular landing area and the number 115 are visible on the ground. But otherwise this marking is not there.
When Will first enters the aliens' laboratory there is a chair beside a control panel on the right side of the room, apparently left on the set by mistake. This human style chair is out place as the aliens' bodies would never be able to fit into it or even be able to do anything but stand upright at all times.
The two statues outside the alien complex are of human form but it was established that the aliens had never seen a human before and therefore would not know how to make a statue of one.
Once Don ordered Dr. Smith to clean the hand guns, he and Will could have easily taken back control of the Jupiter 2 from the alien impostors with the hand guns he was cleaning.