when they checked for mites did they also check for bacterial/fungal infection? these things live in the ear at low amounts normally, and when there is either primary infectinon (from mites/allergies) or growth initiated by moisture, etc...
Ear infections are actually more common to be in one ear, or worse in one ear than the other, there is no connection between the ears so each is an independant instance.
I don't recommend putting any meds in the ear unless directed by a vet, simply because in a worse case scenario, the solution you have may be ototoxic and in bad ear infections sometimes the tympanic membrane (ear drum) is not intact. Putting anything ototoxic down there in this situation = PAIN and likely deafness as a result.
If your pup has an ear infection (as it sounds like it does) let your vet decide what to put in it, and what to clean it with. There are a lot of different OTC and prescription cleaners out there, each one with a different purpose. For example, Oticalm is a drying agent, Cerumene breaks up debris but is oil-base and non-ototoxic, Chlorohexiderm is a great flush but ototoxic etc... and different ear medications specifically for different problems (Conofite for yeast, Baytril Otic for bac/fungal and inflammation, Conofite/Dex for yeast with inflammation, Gentomycin Otic, Tresaderm, etc..) each drug has it's place in a given situation, and no Vet i know would recommend the use of any OTC drugs.
Let us know what your vet says! Also, try not to clean the ears before going to the vet, your vet needs a good clean sample of the debris to give you a diagnosis. If the ear is clean when the vet sees it, there is nothing they can tell you for sure! I know it will bug your baby and you, but if you can, please refrain.