The problem you have outlined is one I regularly come across when people have cleaned their own carpets with a rental "Slug Doctor or similar.
Nearly always it's with a deeper pile synthetic carpet. The carpet will feel dry, but placing a weighted paper towel on the carpet soon shows moisture still present.
Expeience has shown that when the carpet is totally dry and aired, the "dog that needs a bath" malodour disappears.
However, to make the carpet hygenic, sanitising as others have suggested is required.
Safe and happy cleaning
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The JAGUAR 6.6 --"A TRUE INDUSTRIAL SYSTEM"; not a generic squirt & suck!