What was the name of the shot for the ear mites?
Shots (Ivermectin) can be given for other types of mites but they aren't standard for pups with ear mites I don't think.
There can be a smell if it is ear mites. When bathing, it is best to put cotton balls in their ears and possibly use a drying solution when you're done. It helps protect against yeast infections in their ears.