I don't know that levo 'causes' joint pain. I can only share my experience. Doc did a TSH test on me years ago just so we would have a base line because of all the thyroid problems experienced by various family members. Imagine our surprise when it came back at 8. something and I had NO symptoms.
I was totally ignorant re: synthetic vs natural (NDT) and was put on levo. Hypo symptoms developed and worsened even tho they switched me from levo to name brand Synthroid. One of those symptoms was horrible joint/bone pain. It is pain like no other. It seems to radiate from the bone outwards... from deep inside joints.
Long story, short... when I complained about hypo symptoms, an internist suggested that I might not be converting T 4 to T 3 (first I had heard about that) and that NDT might be helpful. Well, started on Armour (this was back in the nineties) and within a week/10 days, the sun came out, angels sang and I was bouncing off the walls in pure joy because almost all of the hypo symptoms had disappeared or dramatically lessened. So... does levo 'cause' joint/bone pain? or is that a symptom of hypo? I guess the next question would be 'do hypo folks experience joint/bone pain in the absence of levo/synthroid, right?