During the sequence where Chipper is choosing between the two caged groups, listen and you can hear the clone-Valerie call Chipper "she". Not only is Chipper male, as established in previous episodes, but the dog is referred to as a male throughout this episode as well. The clone-Fitzhugh even calls him "boy" at practically the same time.
Several strong continuity notes: reference is made to Dan in the Olympics (from "Deadly Lodestone"), the science center from "Genius at Work" is used again, and the knockout hypodermic from "Six Hours to Live" is utilized.