At first you might notice a change in attitude with your bunny, pulling away when you pet instead of the normal loving position you are used to. No, it's not your imagination, it's a warning sign of a problem brewing inside the ear that you probably haven't observed or can see yet.
Once you have had them you know it's a common parasitic problem responsible for the condition known as Ear Canker. Sometimes only one ear is affected. There can be more serious cases that arise with heavy scabbing on the inside of the ear, painful to the rabbit as well as to see. Best to let it come off naturally which avoids adding more pain with removal. Keeping your cages cleaned out is very helpful, but no matter how clean you try to keep everything, your rabbit will eventually suffer from this disease. It can transfer from other animals that have it.
First, to remedy the situation it is necessary to have another person help you. It takes one person to hold the rabbit still and the other person to administer the solution. They are more upset with the problem and less likely to hold still for you, so be prepared when approaching that ear.
Second, my preference for results is Miracle Care R-7M Ear Mite Treatment for Dogs & Cats... yes, you read that right, for dogs and cats. You can get it in the pet store off the shelf or on the internet, price is about $7 - $10 for a 4 oz bottle. It gives immediate relief to your bunny's ears. If it's a really bad case of mites you can use a cosmetic pad soaked with the solution and place in it the ear, hold for a couple of minutes to let it soak in before he/she shakes it out. Use a fresh pad for each ear. Normally a few drops should do the trick.
Third, don't think you are done. Check the next day to see how you are doing with results. It can be astounding as to how fast it works! But the truth is there are eggs from the mites still in the ear and waiting to hatch out. Therefore, you will need to repeat the process in about 2 weeks to make sure they are dead.
No matter how careful you are, ear mites happen and can't be ignored or serious damage to your rabbit can happen quickly.