A perfect God creating an imperfect universe is a paradox.
First of all, notice the 'if' at the begining. I am agnostic, myself.

Second, how can you know what's perfect? What's the definition of perfect? How and when can you say something is perfect? How can you judge, if nothing else is perfect?

That's the problem. Therefore, if there was a God, he'd be exactly that - perfect. It's the ultimate paradox for the ultimate being. I cannot comprehend it... but then again, I'm not God.