Sadly for you, the Mission was not designed for rough riding. It’s mainly a paved trail/street bike.
The fender brace in the rear will bow out, which moves the fender closer to the tire. The bow effect can happen at installation time, or over time while riding. You need to be sure the brace is in a more straight position by pushing in on each side. That will move the fender away from the tire.
If you want to totally stop it from happening, make a couple of extenders out of plate steel, about one inch long and bolt them down at the back wheel where the brace it now bolted. That will raise the rear of the fender up and that should correct the issue.