That's like saying that there's a design flaw because someone chooses to put water in their gas tank instead of gas. Or that there's a design flaw on a keyboard because the "H" key is too close to the "J" key. Or there's a design flaw with a chair because the user tried to sit on the arm and fell over.
The breathing and eating mechanism is a marvel of design and works perfectly 99.99999% of the time. However when someone doesn't chew their food thoroughly and tries to eat too fast then there is a chance that they're going to breathe food. God did design a LOT of safeguards against stupidity, but his job wasn't to insure that life was perfect.
I didn't call it a flaw. I said it appears to be the result of a long series of slight modifications.