I installed a new kohler toilet,the floor levelness was in the bubble both ways,toilet flange was almost perfect,flange height was less than skirt height on toilet,but now I'am off a one half inch side to side on level,has anyone ever encountered a defective toilet with a underside skirt casted uneven

Its rare but possible, I've yet to see one that off. Take it back, nichols trim

Turn the toilet over and inspect the bolt hole areas. You may have picked up some debris or got you bolts cock eyed in the flange. I've never seen a Kohler like you are talking. With the toilet up side down lay a straight edge across the base and measure to each bolt hole. Also recheck your flange at this point for debris like that missing nut from the bolt.