Tradition and magic don't explain interbreeding, unless each time two members of different species interbreed some wizard goes around casting spells that mutate chromosomes or people have the tradition of genetically modifying themselves. It's just plain silly.
Also, people can distinguish infections from other types of discomfort since the Dark Ages. Infections usually involve the activity of bacteria, viruses or other microscopic organisms and are often related to mucus, rashes, rubor, etc. If the researcher would study the problems with Nolthrir ears and not notice any of the previous symptoms, I doubt he or she would call it an infection, since that would be far-fetched.
It could be that Nolthrir got this infection from swimming too fast because they become more vulnerable to an organism that gets to them. I'm not sure if we should consider them to be able to get several infections in the ear in one single week, since I don't know if it's too common for animals to have infections in the same place over and over again without accumulating serious injury.
EDIT: Corrected some text.