Ah ?
I would check that the bearings are set properly onto the swing arm on both sides. (remove the inner race, and check that the outer race is seating properly on the recess.). On the right hand side there is a metal shim used to seal the hole in order for the grease not to fill the tube. Check if it is seated properly and not blocking the outer race to seat.
Then, I would check if the other end of the swing arm is installed properly and if the play between the swing arm and the frame is equal on both side.
If yes, and one pin is still protruding too much, I'm puzzled...