I have a similar set of pocket flares- really poor design, IMO. The floor of the small pocket the screw goes in is not flush with the edge of the flare that touches the side of the Jeep. When the screw is over-tightened it curls the flare inward which pulls the overall flare out of shape. This curling brings the outer lip of the flare inward towards the tire, causing the rubbing. The way I cured this was to go buy some nylon spacers (no rust) about 3/8" thick, if I remember correctly. You will need 30 of them, at least for mine (6 holes in each front, 8 holes for each rear fender). They fill the gap between the flare and the Jeep tub so you don't over-tighten the screws. You could try loosening the screws a bit as a start, but the flares might not return to the correct shape because they are ABS and have a memory to them.
Edit- Of course if only your rear fenders are causing issues, you could just buy them for the back flares.