help me diagnose a kitten killer!

Could be any number of things. The fact that it was "flat as a pancake" makes me suspicious that something killed it. It might even have gotten squished in the garage door accidently. But at any rate, most common predetors are raccoons, possums and other cats(toms esp).
And I agree, kittens don't really need to be outside at night too much. Too many things to eat them, injure them, or carry them off. Small things are food, since to predetors, they aren't "cute".
Sorry to hear of the poor kittens demise, hope you figure out something.
Wolfy