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Sounds like the carpet didn't dry thoroughly. I hope this isn't a mold smell...Could be an odor bacteria smell. I had to get rid of my wall to wall carpet. Carpets trap all kinds of things...
I would have an expert carpet cleaner tell you if the carpet is dry or if it needs to be cleaned again.
Maybe there is a leak somewhere...
One of my dogs had allergies...I changed to organic dog food (dry)- There is no soy, wheat, corn (allergens)..in the food and my pup is doing much better. I wash her bedding in clear detergent only.