then his face should be missing if he shot the bee that startled him
How?

Incorrect, regardless.
cause he said it flew in his face!
Forgive me if I am wrong, but do you slap yourself whenever you swat at something flying in your face?
Apply said logic to shooting at something flying in your face. Not even a dumb beekeeper would point a gun at his own face and fire in response to a bee flying in his face.
The correct answer requires some knowledge on the habits of bees.