I am 61/2 weeks pregnant, taking prometrium (micronized progesterone) (200mg vaginally) for 2 wks. For last 2 days I am having brown discharge after taking it. Is that ok.?

Get a sono done. A sonogram will help to know if the bleeding is ok or not. The doctor can examine you as well. Good luck!
Yes. Likely irritation of the cervix with slight bleeding to create that discharge. An ultrasound with your doctor would be reassuring if you have more questions.