You accidentally left a debug button in! (It's the E key.)
Also, being off-tab makes Jake clip through the floor, making it possible to kill him just by writing a comment while playing this!
Finally, it's possible for the game to ignore my right clicks completely; this kept happening at the bottom of the tutorial level, at the section which taught me about checkpoints. Note: I am playing on a laptop with a touchpad, and I am using the right mouse button on that.