Did you get fitted for shoes at a running store or by someone who is experienced in fitting shoes for runners? You probably need a wider toe box or wider shoe. Our feet swell when we run, I used to have a lot of issues with my feet until I finally found the right shoe for me. I ran 5 half marathons between November 2014 and January 2015, then I had to take several months off because my feet couldn't take it. I had even been fitted for shoes twice before, second time I got put in a wide shoe which helped. Third time was the charm, a few months ago I got a shoe with both a wide toe box and more cushioned shoe and now I'm training again for two half marathons this fall and a full marathon in January. The right shoe made all of the difference!