Breathing faster can be a sign of respiratory muscle fatigue. This type of fatigue means that you have to breathe faster to get the same amount of oxygen you got earlier in your run. Your regular runs may have honed your legs and hips, but not your breathing muscles. Breathing muscles, like any other muscles, can be strengthened. Using a device called an inspiratory muscle trainer for just a few minutes a day can help. You should be able to locate one through a local sports medicine clinic.