M.6.
I've walked around with kidney stones for nearly 1/2 my life at varying times. Sometimes I need to have them taken out (or blasted so I can pass them) and other times I have passed them on my own. I think I currently have 5 small ones that I am waiting to see what happens and have had these ones for nearly a year. As long as I am not in pain, they are not affecting my ability to produce or pass urine, I don't have an active infection, or other issues, my urologist tends to leave them alone until something needs to be done. If the stone gets bigger and starts to cause problems, then your doctor will likely do something, but the sheer existence of stones doesn't necessarily require action.
It sounds like your doctor is doing a good job, but as a mom and your child's only advocate, if something doesn't seem right, you can always get a second opinion.
Make sure they figure out what kind of stones he is producing once he either passes (yikes!) or the remove the stone. That is usually a critical component of determining any lifestyle or diet changes. I actually have an unusual circumstance where I have produced 3 of the 4 types of kidney stones over the years.
Good luck - as a chronic kidney stone person myself, I feel just awful for your little guy and hope this is just a one time thing for him!