Hi, Ying. It does look like external root resorption on your tooth #12. We do not know what the cause of external root resorption is but it its associated with trauma to a tooth. There really is nothing that can be done for the tooth unfortunately. It may be years before you lose the tooth...
Your teeth don't follow the trays, thus they don't fit. You may have to go back a few trays and maybe needs more IPR (interproximal reductions). Hope you saved you last few trays, as it is crutial to go back and see where the problem started.