My bunnies had that exact same thing. I took snowy to the vet and he said it was frostbite! I felt so guilty for letting that happen. Anyways, it could possibly be frostbite. I think your bunnies are housed outside...? If it is, just wait for it to fall off. You can help it along by gently putting a warm, damp washcloth on the ears.
If it is frostbite, it probably happened early in the spring and is just showing up now.
Obviously, if your bunnies are housed indoors or if you live in a warm climate, it's not frostbite and it's probably mites.