A branch falls on Elena's car when she's waiting for the others to return. When Alaric goes back to the car, there's no branch on it.
When Elena pulls the stake out of Harper's leg for Stefan, when they are rescuing Stefan, Stefan's hands are still tied and the rope is trailing over his shoulder, then Damon tells them to hurry up and they are leaving the room and Stefan's hands are untied and the rope nowhere to be seen.