Sorry 180, those black boots at the top of the hatch drain down into the sides of the car. That's not his problem. BUT... it's a good idea to check them anyway. I have one that constantly pops out. I check it every time I open my hatch. If you let water get in there, your rear quarter panels could rust from the insides out. That would be very bad.

Are the stains rusty looking or just dirty looking?

For your sake, I hope it's just a brown leaf that got stuck down into the spoiler drain hole on that side. See my post below about those drains and the lines that feed them. The picture may help you.