Hello Rebecca. I've had s similar problem coughing up a scab-like, brown substance from my throat when I first get up and brush my teeth. I also have a thyroid issue as well. If this substance is not coughed up in the morning I will feel it later when I'm drinking coffee. The heat from the coffee loosens the scab enough to expel it. I'm not sure what causes this and no one has ever told me why it's happening.