Your bunny may have a corneal ulcer, conjunctivitis, a foreign body
in the eye, or other eye infection. He may also have an ear infection
in the corresponding ear. If he has an ear infection which is painful or itchy, he could have accidently scratched his eye while trying to scratch his ear. Or, if the infection is just in the eye (with no ear involvement) the eye could have been itchy or painful and scratching could make it worse by introducing additional bacteria or irritants.