Sounds gross but maybe a little bit of vomit has gotten in there? Xander gets this from time to time. If this is unlikely, probably worth getting checked out in case of infection.
Is it possible he has something stuck in his ear you can't see? Perhaps a visit to the GP to have a look inside is in order. I have been involved in proceedures where we have removed "items" from kiddies orifaces and the only way parents knew something was wrong was a smell. I won't gross you out with examples! Hope it's nothing serious though.
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