1) boxes are not cleaned enough (1 - 2 times daily minimum)

2) boxes are in a location that makes the cat uncomfortable

3) they don't like the litter type - feel or smell

4) cat has an undiagnosed urinary tract infection or other medical problem

5) litterbox is too old. After one year odors are impregnated in the plastic

6) litterbox was cleaned with a chemical cleanser that has an aversive smell instead of soap and water. 

Would you like to use a toilet that isn't flushed?  Most cats prefers you clean the litter box after each use. Felines are fastidious and value cleanliness.

For two-story homes, to prevent your cat from getting side tracked and not making it to the litterbox in time, provide two litterboxes - one on each floor. Provide more than one litterbox in a large home to keep toileting convenient. For multiple cats, provide one more litterbox than the number of cats.

Felines are individuals. just like some people like rap music and others prefer classical, cats have personal preferences. Try different types of litterboxes, different types of litters, and different locations for the box and you will discover your kitten's personal preferences. Try a plastic under-the-bed sweater box instead of a traditional litterbox.

Many cats value their privacy.  Do not place litterboxes in high traffic locations. Would you feel relaxed using a public toilet if there were no stall doors provided?