I do this also.
First, and foremost....if you are having foot pain that is not going away, see a podiatrist. Trust me....the sooner you get in to address whatever is going on---the better off you will be.
Your instinct is right----be wary of doing this with your toe. You may be developing a "hammer toe," which can cause (or be the result of) a neuroma in your foot (read: a pissed of nerve that swelled, moved, and causes pain/numbness etc.etc.). (Welcome to my life!)
Make sure that the toe box (front wider part) of your shoe is big enough. (Or that you aren't cinching it down too too tight when you ride).
Also, make sure you are keeping your heel down (feet flat) when you ride, and not lifting your heel tons and tons. This strains the ball of your foot/puts pressure there, and you may be curling your toe subconsciously as a way to relieve pressure or something that you aren't even aware you are putting on your foot.
Hope this helps. If you have more questions. Ask away!



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