It's entirely possible your child could have an ear infection AND a TMJ issue at the same time.
I would still get to your child's regular pediatrician today and ask for him to be checked for ear infection again, ASAP. I've had some OK doctors at urgent care centers and other doctors who misdiagnosed me, in one case, and my child, in another. I'd really get your pediatrician --who examines kids' ears all the time--involved today. A doctor at an urgent care center sees everyone for everything and may or may not see a lot of younger kids regularly. If your child has ear pain, tell the doctor's office you need a sick child appointment today, and not tomorrow. (If this was a specialist urgent care with pediatricians that might make you more confident but if this was the doctor on duty, I'd get to your own ped.)
If there is an ear infection, it's not at all like a cold that resolves on its own and if you let it wait it can cause larger issues like possible hearing loss. Ear infections need antibiotics starting as soon as possible. Ear infections can appear to go away but still be lingering without any noticeable symptoms..
BTW, colds often are the start of an ear infection; a kid has a cold, fluid fills the tubes in the ears due to the cold, and sits there and gets infected. Our pediatrician told us that ear infections are usually "secondary infections" associated with colds or sometimes bad allergies etc. but they are not the same thing as a cold itself and require different treatment.