My son has swollen nodes behind one ear. Verified no infection in that ear last week. He has scratched the inside.?

Get examined. If your son has lymph nodes swollen for weeks it can be from the skin being injured but i would make sure there is nothing more scary. There are other things like "mono" that can give you the same finding but get checked.
Most likely nothing . Swollen lymph nodes behind the ear are usually benign. They can occur because of acne, skin infection or bug bites. If it stays enlarged for more than a few weeks, or if there is pain or redness you should see a doctor.