Near the beginning Will pulls Dr. Smith out of the cosmic dust quicksand and Smith's shirt and pants are covered with cosmic dust. The frame jumps and Smith is now knelling near the pit and his shirt and pants are perfectly clean.
In order for the alien to understand Dr, Robinson the Robot was needed to translate, however later when Will is explaining to the alien why he took his space ship the alien understood him without the Robot translating.
When Will suggests to the alien that he take Dr. Smith back up in the space vehicle in order to "change him back", the alien agrees and begins putting Dr. Smith back into the craft - yet Will strenuously objects, saying "Don't take him away!" even though he himself had suggested it.
When Will and Penny sit down to play chess, he (playing black) tells Penny (playing white) that he'll let her take the first move. Every chess player knows that the person playing white always goes first.