I used to get some allergy & exercise-induced asthma symptoms when I was younger, and it would hurt in the area you're describing -- upper chest, bottom of throat.

If you're allergic to something in the air, AND you're breathing a lot because you're doing aerobic exercise, you're increasing your exposure to whatever is irritating your lungs.

Maybe ask a doc to listen to your lungs if it doesn't clear up in a few days?