I experienced the same problem last night. My window went up a little more than yous did, but the window track was hitting the outer belt weatherstrip (fuzzy). Once I pulled out a little it rolled right up. I figured it was my repop doors. I think it will work itself in because it was barely hitting. It was just enough to catch.
I operated the window after each piece I installed to make sure it would work fine.
The one thing I don't like the most is the window track is slightly visible once it is rolled up. Most people will not notice it.