John realizes that Sherlock is, well, a cat. His eyes, his feline grace and attitude, his taste for milk and the way he likes to stretch out on the sofa, the screeching noise he makes with his violin... So doesn't it make sense to try to break him of bad habits the way one would do with a cat? Hence John breaks out the water spray bottle.
This fic is genius.
Pussycat Pussycat, or How Your Sherlock Learns, by sevenswells