I have a theory about prevent defense not working so often and that is that it is never practiced. It's also a bad strategy, but coupling that with the fact that the players aren't really in their comfort zone running it sets it up for allowing the thing it is designed to prevent.
When you tell the other team you're not even interested in getting a first down, you just want to run it three times and punt, then it'll bite you in the ***. They did it TWICE.