Being John Malkovich (1999)
Director - Spike Jonze
Shortly after John Malkovich meets Craig Schwartz (John Cusack) on the side of the road he wanders off mad. As he does, a car passes by with a man leaning out the window. The man throws a can hitting Malkovich square in the back of the head while yelling, "Hey Malkovich! Think Fast!" - causing the Oscar nominated actor to scream out in legitimate pain.
Neither the can throwing nor the reaction were scripted but the drunken extra in the car felt the opportunity was too good to pass up. Jonze thought the scene added to the character's frustration and left it in.
Instead of being fired, the extra was added to the final cut of the film and given a raise.