My 16 year old has lived with us for the whole year. I support all his expenses, food clothing and so forth. But my girlfiend and I split the utilities and mortgage right up the middle. Since I support my son, and she cannot claim him as a dependent, shouldn't I be able to file HOH?

You would if you paid a penny more for household expenses ('the cost of keeping up the home') than she did.
So quick TODAY pay for something without her, or reimburse her.

We really haven't tracked it, I am the one who buys most of the groceries for the household. She actually makes more money than I do, but most of her pay goes to her student loans. I don't believe I am doing anything wrong here, and according to my online filing company that I use, it seems to be suggesting that I qualify for it. I did not file Hoh last year, although I did have my son with me for most of the year and claimed him as a dependent. Will the change in status trigger a red flag?