The rule of thumb is to have one more litter box than number of cats. And don't locate them all in the same room! They need to be spread out in different places. Cats will encounter "situations" that stress them out - most you aren't aware of. For example, let's say one of your three cats is sitting in the window enjoying watching the birds and a stray cat walks across your yard. Your cat is feeling very threatened and protective of his territory. He may begin "guarding" the litter boxes from your other two cats. He doesn’t hiss or raise his back, he does this VERY inconspicuously... he will sit calmly at the door of the litter box room and the other cats pick up on his subtle dominant postures, but you don't. The other two cats won’t walk past him into the room.
Cats are also very sensitive about things we don’t even think of. Maybe there’s a scented candle in one of the litter box areas and one cat is repelled by the smell. You never know, but you MUST give cats choices. And that includes using different boxes in different places. This will make for happier cats and help to eliminate future litter box issues.