Yep, a friend of mine couldn't tell the difference between eggs and air bubbles in fecals. It takes a trained eye to find things like coccidia/crypto and giardia. Pinworm eggs are pretty easy to see though, they're fairly good sized.

I've found digested pinworm eggs in some of my snakes' fecals. I'm guessing it's from the mice. The snakes have never come up positive for anything.