Jaw clicking when doing tongue exercises?

I feel a "clunk" on the inside and when I put my hand near and on my tmj areas when doing tongue exercises given to me by my physical therapist. I have muscle based tmjd. They've helped a lot but I have a lot of creptius and trigeminal and occipital Neuralgia on both sides, but mostly my left. I turn my head and I hear and feel clicking in my neck. I think the tongue/jaw exercises help but the clicking is a little worrisome since I can't tell if it's muscles being tight and feels more like a structural issue. Anyone relate?