The reasons may be complicated: we used covered litter boxes but at some time, Tigris attacked Filou every time he was in the litterbox and so Filou looked for another solution and peed in some hidden corners in the apartment (no longer hidden then). Now we have open litter boxes and Filou doesn't feel so fenced in anymore and it never happened again. (They still hate a used litterbox. If it's not ok Tigris stands in front of the litterbox and gives a rough meeeaooo (meaning: Do ! clean the litterbox).)
Is your young cat bullied by others?
I wish you good luck and patience -there is a reason why and you can find it. (I had to tell that to me quite often because it took about a year to solve the problem)