My 3 year old is always scratching his head and I was looking at his scalp and feeling around and felt a few small lumps in the same area, I'm worried.

Sounds like lice, fleas, or bedbugs. Do you have pets? Does he go to daycare? Have you looked for any bugs on his scalp (and any pets)?
One other option might be folliculitis (blocked, inflamed hair follicules).