I think someone may be having some dominance issues here - cats will do this if they want to be "king of the hill."

Many cats like to urinate in one box and defecate in another so your vet is right about having one box per cat plus one extra!

If this continues, you will have to take steps to try to figure out the instigator. I suppose you could isolate one cat and let the other two roam for a week, then change the mix and use the process of elimination (sorry I don't really mean to make a pun here!) to figure out who's the culprit. Then you could get a vet check just to be sure this isn't a medical issue.
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Smile, it will make them wonder what you are up to!

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