I've had any number of students around her age with similar issues, and as it happens I also have some small understanding of human physiology (40+ years as an ER/Flight nurse and an MS in Human Physiology). It is, as your Dr says, quite likely a combination of "growing pains" and TKD training. Not much can be done about the first, really.
The way martial arts teach movement is, at least in theory, optimized. But that assumes "normal" anatomy is universal (it isn't) and that the production tolerances for human anatomy are as tightly controlled as the finest mechanical devices (it isn't). So tiny, otherwise unremarkable, variations in anatomy can cause these "optimized" movements to be anything but, especially given the added force and extended range of motion MA students strive for.
So how do you fix it? Technique. The instructor needs to work with the student to find what it is in the various movements that is causing the pain, and work with them to modify those movements for their unique physiology. Once those modifications are identified, they need to work with the student to ingrain them into muscle memory.
In short, if it hurts, YOU'RE DOING IT WRONG.