First of all, the mutations don't have to coincide. So long as two creatures are still able to mate the new characteristics can be passed down. Secondly, I'm sure mutations developed that were both detrimental and beneficial, but that's where natural selection comes in.
It's not that I don't see what you're saying, it's just that I see "oh... well God did it..." as the ultimate cop-out. And it doesn't really explain anything, it just generates more questions.
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