A metatarsal fracture can come in two forms. A clean fracture, or more likely a greenstick fracture, which is a partial fracture. Swelling is the norm. They take about three months to heal. What you have is called a "focal finding". It is very likely due to the inflammation secondary to the injury. Normally immobilization with a plaster cast for a short time is prescribed for such a fracture. The x-rays are often inconclusive. If there is no cast elevation and a rubbing of a cortisone cream on the foot will help. In the case of such injuries the idea is to avoid the swelling by an immediate wrap with an elastic bandage wrapped circumferentially and overlapping snugly, but not too tight. Once the swelling takes place it's hard to get it down. Unless there is numbness, blue color, or loss of sensation it is unlikely there is a clot, especially if your dorsalis pedis pulse is strong. Numbness and blue color are hallmarks of arterial oclusion. A podiatrist is probably the best medical professional to consult. They are sometimes looked down upon by the rest of the medical profession, but they know everything possible about the foot.
When you can, elevate the swollen leg to help drain away the build up of fluid.
Only by a medical examination will you get to know what is causing this ongoing problem.
Best wishes.