Don't ignore the problem!! You don't want to cause any long term damage in that precious area... Plus, why suffer if you can fix this?

As everyone said: cleat alignment but above all I'd say shoes too tight. Your feet get a little bigger as you ride, so loosening the velcro after 15 miles may be a good idea. Wiggling your toes once in a while (like: every time you drink?) and stopping for a little walk when possible is also a good idea...

Enjoy!