When a nerve is inflammed or swollen, the bones in the ball of the foot (metatarsals) will put increased pressure on a nerve and you will feel the nerve pop up and down in the foot.  This "clicking" is called a Mulder's Click and will often be confirmation of a neuroma in that area.  A neuroma is a common cause of ball of foot pain.

Brandt R Gibson, DPM
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Podiatrist, Neuropathy Doctor, Father of 11 and Founder of Mountain West Foot & Ankle Institute