I read the OP's question differently and think that even after basic tweaking of the fenders, during a ride they wiggle around, not holding any preride adjustments and rub. Is it minor rubbing that is more annoying than hurting performance?

Maybe in an effort to save weight (cyclists and their weight concerns), the fender manufacturer used fender stays that are a little undersized. Look to over bend a little or reinforce the weak points or if it doesn't hurt performance, ignore it. Worst case scenario, replace the offending fenders with better ones