It is a well-known reaction and the company that makes the vaccine lists it as a side-effect. My bunnies have not reacted in this way to the nobivac myxo-RHD-vaccine, but one of them had a reaction to the cunivak vaccines that preceded this vaccine. He developed small, superficial sores that needed a whole month to heal. I rinsed with saline and used antibiotic cream on them twice/day.
Any wound can of course get infected and need treatment with oral or injectable antibiotics, so I’m glad you have a vet appointment.

I used polymyxin b. You can also use fucidine.