I get hot spots on the ball of my feet. Basically it is caused by a repetitive chafing motion on the ball of the foot. I had callouses, so it was basically the callous moving around independent of the foot under / above / behind it.

Last year it was really bad I ran the full diagnostic series...

1) Sanded my callouses so they wouldn't provide a hard pan that can be moved back and forth over my - problem persisted.
2) Replaced insoles - problem persisted.
3) new shoes - problem persisted, but improved.
4) new cleats - problem persisted, but improved more.
5) new pedals - problem solved.

In retrospect it was a combination of old / worn equipment:

1) my shoes were old and stretched allowing my foot to move around.
2) my cleats and pedals were worn, particularly the flats on the pedals, which was allowing the shoes to wobble on the pedal decks, causing a side to side chafing on the bottom of the foot.