I went back to the place where I got my shoes, and a woman who works there said I should make sure on my next pair of running shoes that there is mesh on that spot of the shoe, which will allow my foot to relieve the pressure. Right now I only have mesh above and below the spot.
They have a podiatrist who comes in twice a week, so I will check with them. My GP didn't even come up with bunions when I talked to him the other day. He said I just needed arch support. Boo.