Spotting, BC pills, concerned

So I've been on BC pills for 4-5 months, I switched off the Depo shot after being on it for approximately 6 years. I've never missed a pill and my periods came regularly until this last one. My period was supposed to start on 9/14, but didn't start till 9/16. It ran till 9/21. I thought I was good until 9/25, I've been spotting since then. It's now it's 10/5. (My next period is supposed to start next week.) It started really light with like no flow with this dark brown almost black with blood clots and has started to switch between this and normal red blood, but a lot heavier. I've already called my doc and they said to give it 2 months and I may need to switch my BC pill. Has any one had this happen and if so did it get straighten out.