When Nexus sends the androids to get the real Smith from the Jupiter 2, he says, "Even your force fields cannot stop us." But when the line comes from the android, he says, "Even your force field cannot stop us."
When the aliens were frozen, one of the girls blinked and bodies could be seen swaying. Dr. Smith bumped into one and she moved.
When back at the Jupiter 2, the duplicate Smith invites everyone to call him "Daddy Zack." When the real Smith returns to the camp, Penny says: "What's wrong, Uncle Zack?" Penny saying "uncle" instead of "daddy" had to be a mistake that was allowed to pass.
During the opening sequence the reflection of studio lighting equipment is visible on the orb atop the crown.