Try hitting the dimpled area with a heat gun for a few seconds. Not long enough to reshape it, just enough to get it hot. That might relax the damage a bit so it requires less filler. You should also rework how your knees sit. Try attaching them a touch higher (maybe a half inch or so) and running a reinforcement strap from the center front of the knee up to the thigh (or waist, inside the flightsuit, if you don't have thigh plates). That way, when you kneel, your actual knee will bend UNDER the plate, and when it touches ground, the plate itself will be resting upright on the ground rather than between knee and ground.
I had the same problem in the past. That's how I fixed it. That and a silver paint marker and some red-brown drybrushing to make the damage look 'real'. Authentic weathering.