Coccidia can be a tough nut to get rid of--or at least, that's our experience with our dogs. A dewormer won't help with coccidia, since the organism responsible is a protozoan. If I'm remembering correctly, the drugs given to get rid of the organism just keep it in check until the animal's immune system can control it--and stress or illness or other things that stress the immune system, can cause a flare up. It sounds like your cat needs another round of treatment.
And, yes, keep puppy away from the litter box! Coccidia cysts are shed in the feces.
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