The emotions you mentioned you feel all the time in your query- stress,anxiety, nervousness- are the reasons why TMJ usually occurs. With the help of orthodontic treatment the teeth alignment becomes proper which helps in establishing correct path of treatment but since TMJ is a syndrome it never goes completely. The important thing is that TMJ should remain asymptomatic and there should not be any pain or discomfort to you by it.

Orthodontic treatment changes the relationship between your upper and lower teeth which is called as occlusion. Change in the occlusion corrects TMJ but can also cause some discomfort till you get adjusted to the new occlusion pattern. Don't get panicked. I would like to know if you have any pain related to TMJ or do you hear any sound while opening and closing your mouth. You also mentioned that you are in second phase of your treatment. I would also like to know that are your teeth removed for braces treatment? As Orthodontic treatment is a gradual process, patience is needed from your part. Meanwhile, don't forget to smile.