Towards the end of this seasons premiere Peter Bishop follows gunshots to Charlie who is with the nurse's dead body. At the end of the premiere we see Charlie (now apparently the shape-shifter soldier from an alternate universe) putting Charlie (who he seemingly killed while taken on his identity) into the hospital furnace. Learning this we must assume that the shape-shifter hid the real Charlie's body and retrieved the nurse's body to set the scene before Peter arrived. This is quite of feat...leading us to believe that the shape-shifter is capable of moving extremely fast.
What should raise red flags to Peter and Walter is that there is not a second body found for the nurse. If the shape-shifter had been killed as the nurse there should also be a body somewhere for the real nurse (from whom he stole his identity with the three pronged mechanism). I wonder if this will be addressed later on? Knowing Peter and Walter's characters this is a detail that they would not overlook. To me it seems that the writers sacrificed a consistent storyline to create a dramatic ending.