If you loosened inner screw on factory cross bars too much...
If you loosened inner screw (there are 2 on each end, one is shorter (inside), another one is longer (outside). Longer one goes through metal thingy in the tower, shorter one doesn't) on factory cross bars to the point that it seems it's out of the thread and you can't get it back in here is what you do:
Remove outside screw (the longer one) completely. This will allow you to remove metal thingy that it holds. Now you can turn over the cross-bar and see how to install inner screw correctly - there is a plastic octagonal shape in which the nut on the inner screw should fit. I couldn't get it back in without removing metal thingy to see what is inside. Now you can install outside screw back - this is easy.