My kitten seems to scratch behind his ears quite a lot too. The vet checked him for ear mites but he was all clear. He's had flea drops too so shouldn't be that. He has a little wax in his ears but won't let me near them to clean them! I think he must just like scratching - he di it more when I put a collar on him though, think he was trying to get it off (he succeeded eventually so I've given up on it for now!)