Morton's Neuroma: This condition involves a thickening of the tissue around the nerves leading to the toes, causing pain, numbness, and puffiness in the ball of the foot. The symptom of feeling it when flexing toes aligns with the typical presentation of Morton's Neuroma, as this action can exacerbate the pressure on the affected nerve.

Plantar Fasciitis: Inflammation of the plantar fascia, a band of tissue supporting the arch of the foot, can cause pain and swelling in the heel and the ball of the foot. While it primarily affects the heel, the pain can radiate, and swelling might be felt in the ball of the foot.
Metatarsalgia: This condition is characterized by pain and inflammation in the ball of the foot, which could be due to various factors including poor foot mechanics, overuse, or ill-fitting shoes. It could cause puffiness due to inflammation.
Bursitis: Inflammation of the bursae (fluid-filled sacs that cushion bones, tendons, and muscles near joints) in the foot can cause swelling and pain, potentially leading to a feeling of puffiness, especially if the bursae in the ball of the foot are affected.

Deep Vein Thrombosis (DVT): Although less common in the foot, DVT can cause swelling and pain. It's crucial to consider this diagnosis due to its potential for severe complications, such as pulmonary embolism, if not promptly treated.
Infection (Cellulitis or Abscess): Bacterial infections can cause swelling, redness, and pain in the affected area. In the context of the ball of the foot, an infection could lead to significant morbidity if not addressed.
Diabetic Neuropathy: For patients with diabetes, neuropathy can cause a variety of symptoms including pain, numbness, and swelling in the feet. It's essential to consider this in diabetic patients due to the risk of unnoticed injuries leading to severe infections.

Lipoma or Other Soft Tissue Tumors: Benign growths like lipomas can cause localized swelling and might be felt as puffiness, especially if they are located in the ball of the foot.
Gout or Pseudogout: These conditions involve the deposition of crystals within joints, leading to inflammation and swelling. While they more commonly affect the big toe, they can affect other areas of the foot, including the ball.
Charcot Foot: A condition seen in patients with significant neuropathy (often due to diabetes), characterized by a loss of sensation and subsequent destruction of the foot's bones and joints, which can lead to swelling and deformity.