Thank you for writing!
Did you get your period after the spotting? If so, then you can't be pregnant. Many periods start off with brown discharge and since you are on the Pill a year now, you may not get periods at all - just a bit of discharge for a few days every month. This is normal and this is not a sign of pregnancy. I'm not sure why your doctor said this. You also can't get pregnant if you aren't having sex.
As long as you are taking the pill exactly as prescribed, you have little to no chance of pregnancy. You can take a test to reassure yourself. You might want to consider changing your doctor. Listening to patients is a very important component of health care.