On the bottom cover, underneath the trans, it looks like an access cover was never installed. Is it missing, or just not used on the Prius application?
Do you mean the hole to the left of the oil change door where you can see the transaxle drain/fill plugs? I don't think there is suppose to be a cover, at least mine has never had one. It's just a place where the transaxle fluid can run out when you change it.
I've put some duct tape across the hole that looks like it should have a cover - it's on the passenger side toward the front. I figure nobody will see it anyway, and the duct tape is holding up.