It's his own weird way of letting her know. It's not something everyone is aware of, after all. But Bruce has studied physiology, the way bodies work and how to properly master his own. He is the definition of the control freak.
"Like the Kents took in Clark."
He tries not to think too long on Martha, on how scared Clark had been to lose his mother. At least he had been able to deliver on that promise and save her, it was one way he didn't fail Clark.