Rabbits as a rule get mites from their mothers. The rabbit’s immune system keeps the number of mites down, so they cant cause any trouble. Then if the bun experiences stress of some kind (it doesnt even have to be negative stress), the immune defense takes a (temporary) toll, and the mites seize the opportunity to multiply.
So is not about the hygiene in your house. Its still wise, of course, to do thorough cleaning, wash fabrics and freeze toys etc for 48-72 hours, after the bun receives treatment. The bun should get repeat treatment after 8-14 days in order to catch the mites that were eggs when you did the first round. For heavy infestations, the bun might need a 3rd round of treatment.
If you look at the skin under the fur where he scratches, do you detect any sort of problem? Fur mites typically cause skin-colored (yellowish-white) scabs/crusts and flakiness. The skin of a rabbit should be completely even in texture, soft and pliable (except on the face where you can feel small hard-ish “knobs” that typically encompass a whisker.)