I'm 9 weeks pregnant and been on progesterone vaginal gel. Having brown/salmon discharge with clumps. Is this normal or should I call doctor?

Your doc should. Have explained that to u- what to expect, in my pts it is common to get that, but u should call your doc as your doc may or may not want to check you, and i assume you already had an ultrasound to check fetal viability because if you haven't u need one now , and in the future if your doc puts u on a med like that your doc is supposed to tell you what you could expect from taking it.
Could be. This sounds like old blood, but any bleeding in pregnancy you should always inform your doctor. I'm assuming you are having clumps of left-over Progesterone gel, and not blood clumps. Definitely make an appointment. An ultrasound will ease your fears for sure.