Chemical or has my cycle not regulated itself!

My husband and I are TTC so my last depo shot was this past March. The shot would last until about the end of June to the beginning of July. My cycle appeared mid October for about 4-5 days with normal flow for me. Then I began to spot dark blood for 4 days beginning the first of November. It returned this past Friday with normal red color and flow. The week before I was experiencing breast pain and tenderness, reflux, fatigue, and back pain. When it started Friday I was experiencing nausea, back pain, and cramps. I had more clotting than usual. Before it started I took an at home test but it was negative. This is day 3 and it's now super light. Could I have had an early miscarriage that was too early for the test to pick up or is my body still trying to regulate itself? Any advice would be helpful. Thanks.