Maybe Stephan returned to the townhouse to get the other white croc. If he dressed her and carried her to his car, one of the crocs could have fallen off because crocs do not fasten to the feet. If he didn't notice it was missing until after he drove to the school, he could have decided to go back for the missing shoe (and the clicker). At that time Jenn was up helping with the dog, so he couldn't get the shoe without questions being asked. Maybe Jenn saw the shoe on the floor and picked it up thinking Maddy dropped it there. If Monday was gym day at school, Maddy would also have needed tennis shoes anyways.