I was diagnosed with FAI in both hips when I was around the same age. I had my right hip done a couple years ago, then had my left hip done a little more than a month ago (I am 18 now). Although I'm not a doctor, I do know a lot about it.
Just from reading what you said, it could be a few things. 1) the surgeon wasn't very good and did a poor job 2) The surgeon missed a few things. FAI can cause other things too like torn labrums, loose bodies (bits of torn cartilage floating in the joint), and synovitis (joint capsule inflammation). It's possible that he got rid of the bone deformity, but didn't fix the other thigns. In addition, there are two types of FAI: cam and pincer. Pincer is a deformity on the acetabulum (socket) and cam is a deformity on the femoral head (ball). It's not uncommon to have both kinds, and it's possible the surgeon only fixed one of them, and not both. 3) since you mentioned how you got another x-ray showing the bone that supposedly was gone had come back, it's possible that your son has "heterotrophic ossification" which is just a fancy way of saying that the bone was shaven in the hip, but it grew back. Although not common, it does happen after some FAI surgeries.
My advice is find the best sports medicine surgeon you can and get and MRI arthrogram of your son's hip. The MRI is much more advanced than an x-ray. Sometimes, x-rays will not pick up on FAI, as was my case. In addition, MRI's will see any soft tissue damage, and the "arthrogram" part is a dye they inject to see if there's a torn labrum.
Best of luck, let me know if you have other questions.