I was having a problem recently with one of the 3 cats peeing outside of the box, and did one pee/poop.....I was about out of my mind. I did some investigating, and found that what i believe was happening was that Stephano was ambushing Taffy while he was trying to use the litter box. Also, I had a Breeze litter box (which I love because I HATE litter tracking), however, my boys were less enthusiastic about that litter box and would only pee in it. So I moved that litter box into another room and put a regular littler box (covered one since neither seem to mind using a covered box) and put in WBCL in that box. I also added a 4th litter box. The boys only have access to 3 boxes, Beep is not out with the boys since she is vicious, so I figure with them being able to get to 3 boxes, hopefully that would stop it, and so far it seems to have worked. What I noticed was that Taffy is one of those cats that doesn't seem to go very often to the litter box, but he usually goes immediately after he eats in the morning, he pees a river and he usually poops. So I have Stephano put up in another room while Taffy eats (otherwise Steph eats his food) and then I give Taffy enough time to get to the new box, which is a big rubbermaid container with 40 pounds of Arm and Hammer Ultra Last litter, which they seem to love.....this 4th box has become THE box of choice for them. Some people would protest having that many litter boxes, but it is actually easier, because they seem to pick one box to do the most business in, which is this huge box, and the other ones I can go longer without having to completely clean them because they aren't getting that much use, so it's really not that hard to have that many. The new box is just open, no lid on it, and they seem to do fine, it's out of the way and the A & H litter is doing great odor control, btw. And I was about to lose my mind because taffy peed on my couch in two different places, which one day peed on my dogs bed AND took a big poop. I was out of my mind. I cleaned everything with tons and tons of vinegar and hot water and dry cleaned covers, and it's been about two weeks now, and knock on wood....we have not had any more problems. I would rather have 10 litter boxes scattered about my house if it meant they wouldn't resort to going on my furniture.
Good luck! Maybe you could play detective and see if one of the cats is pestering the other one, or maybe that box is just in a place that whoever is doing it just doesn't feel comfotable? Taffy is a big chicken, so I think it was a combination of him being afraid of something and Stephano hassling him while he was trying to go.