applied it to the back of my iPhone 4.. applied just about as perfectly as I could and there are a lot of blotchy areas. They don't look like dirt they just kind of look like rough spots/patches if that makes any sense. Do those go away?
If you applied it correctly and didn't leave any fingerprints, those are probably just microscopic air bubbles. I had something similar to what you're describing on my previous phone and it went away in about 24 hours.