After the first episode, interviews with the eliminated contestants were added to the end of each episode to ensure viewers that the cast members weren't really dead. They're still in the makeup used to make them look like a corpse, and talk about leaving the competition and how they felt about the specific way they had to pretend-die.
Zuiker told me he resisted the change: "I was very against that from the very beginning, but I really had no choice because apparently America was quite confused early, and we lost a 1.3 million viewers, so we had to make some adjustments to see if we could get those viewers back."
Still, some people were still confused about whether or not Whodunnit was killing its contestants.