Mites can come in on hay. But buns can also carry mites with them from when they were babies. The mites exist in low numbers and don’t make any trouble, the bun’s own immune defense keep them in check. Then something happens that challenges the bun’s immune defense, and the mites seize the opportunity to start multiplying. You get symptoms like white crusts, dandruff-like flakes and sometimes, but not always, the bun starts scratching itself.
The best treatment is Revolution (selamectin) or ivermectin. Both meds are prescription only unless you’re in Australia. They are highly effective and bunny safe.
And now the warning we always give whenever someone mentions mites or other skin parasites: Never use any compound containing Fipronil on buns. It’s deadly toxic to them. Many different fipronil-containing preparations are sold OTC for dogs and cats, so they’re readily available. They’re safe for dogs and cats, but must never be used on rabbits.