You know, lots of actors use stunt doubles. Like Bruce Willis in the Die Hard movies, or Daniel Craig in the Bond movies. Also it's a common theme on BGT that, as you progress through, the production gets bigger and may involve "extras" such as singers or dancers that were not in the original audition.
I don't think Jules was trying to deceive anyone. She is capable of telling one dog from another, and both dogs were in the semi-final so at the very least the judges should have recognised both dogs in the final too.
The act was entertaining. You can only imagine the hours that went into the training those dogs. I thought all three performances (original audition, semi-final and final) were brilliant. If you have any doubts about Matisse, here's his first audition that featured only him - I thought it was amazing how he was capable of acting "away from" any human, on a strange stage, without being led, just on stage on his own.