That's called ultrasound. It's typical for many injuries, although I'm not sure why they'd still be doing it at eight months post Tommy John's. (I've had TJ surgery as well). If they use the wrong settings it can be painful, but I haven't heard of someone having pain the day after. I'm no expert though, so I'd ask the P.T. what's going on.
If they did deep tissue massage on the inner elbow, he could definitely be in some pain. If this is the case, tell the P.T. to take it a bit easier. You could/should be sore after the first few times, but you shouldn't be in "intense pain."
Hope this helps.