I use the igloo boxes too! lol My cats are good about going IN the box. The exception being my oldest (just turned 6) who will poop outside (on the mat, yay polite kitty!) but only when his butt hurts, lol. He has anal gland issues so it's his way of letting me know he needs more of his baby-food (for fiber).

Maybe yours is very picky about the cleanliness of the box? And it's his way of telling you to clean it?