A brown vaginal discharge combined with itching could indicate a vaginal infection. Not all vaginal infections are sexually transmitted. Vaginal infections (like thrush, for example) can be caused by fungi or bacteria that normally live in the vagina but from something that decreases the local immunity, they cause infection. You may want to request vaginal examination, pap-test, and microbiological examination of a vaginal sample. You may want to consult your gynecologist about this.
That spotting, you had last month, is probably due to missing those 3 pills. By missing them your estrogen level decreased and that usually causes bleeding from the inner womb layer (endometrium).
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