Does your litterbox have a hood or is it a flat tray?
I wonder if your kitty actually IS in the box, but has his bottom hanging over the edge and the poop lands beside the tray on the floor. Another cause, if it isn't from him hanging his butt over the edge, is some cats prefer two litteroxes, one to pee in and one to poo in.
So, you can try using two boxes and/or use litterboxes with hoods to keep him contained in the box. Most cats that use litterboxes with hoods will step inside and face out to 'go', thus depositing their business inside where the sides of the hood contain them.
Good luck, and let us know what works for you and your kitten,