I had the same problem on my '08 Expedition. I had intermittent, slow water leak from between the top of the hatch glass and the weatherstrip. I have been to the dealer a total of 15 times, and it still leaks. So far they have tried:

1) Change weatherstrip (at least three times)
2) Make "adjustments" (numerous times)
3) Change out the glass window.
4) Change out the entire hatch assembly.
5) Bend out the flange on the hatch.

Guess what... still leaks. They told me that they never heard of such a problem before.

I have considered just caulking the hatch window shut and disengaging the latch, so it will never open - but I am concerned about dirt/leaves/debris building up in the dead space, which can lead to rust and corrosion - if I seal the window shut.