I have had the same story, dentist screwed up and I soon ended up with terrible TMJ pain. It got very-very bad, my teeth, jaw, neck and all the way to the lower back. A nightmare. I later got the top braces and pain lessened in a few weeks. It stopped alltogether when I got the lowers. Now, about 2 months with the lowers, it kicks in again. I also feel that my bite constantly changes and it coincides with the pain spurrs. Interestingly, it is now on the opposite side of the jaw mainly. Although I don't know for sure, but I think that my muscles got out of balance and now they normalize, that is what I hope

I also see that my jaw is kind of slanted, so I am assuming that I will be through pain again as it comes back to normal.
That is my experience, but based on that, I suiggest you wait a little and see. I know I hate this waiting game myself, but unfortunately, that is what we have to do with braces. I wish you feel better soon!
Had full mouth metal braces for 21 months. Debonded April 2013. Now wearing clear plastic retainers every other night.
I have no formal dental or orthodontic education. Hence, all opinions expressed by me on this forum are those of an "informed consumer" and by no means intended as an expert advice.