Cloning would not reproduce memories.
When the giant scientists use the "floor suction" system to recapture the fleeing Spindrift crew members in the ductwork, there are several points at which their hair (especially Valerie's) is blowing directly away from the direction they are supposedly being pulled by the suction.
When Chipper is trying to decide which are the real castaways and which are the clones Valerie refers to Chipper as "girl" while the others refer to him as "boy".