This sometimes happens with teething. If he has any that haven't fallen out, even though the adults ones have come in, that can trap junk in between. Just keep brushing and if he has some that don't eventually fall out on their own, you can have them removed when he gets neutered so that he only has to go under anesthesia once. They aren't as solidly connected to the jaw as adult teeth, so they have a much easier time healing.
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