No the flairs are not causing any issues , and actually they are all that's keeping the new wheels and tires with the new offset inside the fenders.
Plus I am huge fan of the flairs, I think the wheels and tires would go back to stock before the flairs would come off. Lol.
Toyota actually made the flairs to work around or in conjunction with Toyota flaps, the rub is back inside the fender on the inner side of the flaps.
I can trim the inner flaps or try and heat them up to attempt to reshape, and fix the rub. I would rather not, if I can get the alignment to cure it.
If not I could also just let it eventually wear through the flap. However it only rubs when backing up with the wheels cranked, it could take quite ca long time to wear through.
If it's rubbing in reverse, the fix is super easy. Refer to my post here -
Trimming Wheel Well for Larger Tires