so this seems strange, but I want to turn my Hydrus pet back to common. when I click 'use on Aepona' it tells me its an invalid combination. what am I missing here?

The common potion has never worked... :( You could always pound him and readopt him since that would turn him common.

so... why does the common potion not work? doesnt that seem really strange? is it an old glitch that has never been fixed? if so, why?

It's just never been been fixed, only someone like Alx could say the exact reason. File a ticket and a UA will change the pet/delete the potion.