Movie/TV universes re-use actors in different roles all of the time. Like, "Pulp Fiction" and "Reservoir Dogs" exist in the same universe, and yet 3 of the actors are in both movies as different characters.... It literally affects nothing except your OCD minds.
Pepper appearing in "Freakshow" will have absolutely no effect on the events in "Asylum" so I don't see what all of the bitching is about. It's not a plot hole. It has literally nothing to do with the plot...