I'm not sure about this, but it might be the type of insulin he's on.
I'm taking lantis, and my injection site is always red, puffy and painful for a couple of hours after I inject, which my doctor says is not supposed to happen. She thinks that the particular type of insulin I'm taking may be too acidic for me, and it's irritating my skin.
It could also be your needles. If they are unsterile, they could cause pain or infection at the site, or if you're not being careful enough when opening them, the tip of the needle could become warped or broken. It sounds like something you'd notice easily, but sometimes I scrape the tip of the needle on the cap when removing it, and when I go to poke myself with it, It hurts tremendously because of a microscopic bend in the tip.
If this has been happening to your son since you started on a particular bottle of insulin or a particular box of new needles, it could be a bad batch.
This is all just my thoughts, and it's nothing compared to the advice of a real doctor, but I hope something I said might help.