Confused ????

So I recently went to my OBGYN to get some help because my partner and I have been struggling TTC on our own. I was given a prescription to start taking at the start of my period. I am now two days late and just started having very faint spotting like a brown light pink in color. I called my doctor to ask if I should take the medication although I am not necessarily bleeding. I was told yes. I did take a pregnancy test first to see if I was pregnant and it read negative. I’m so confused with how my body is working right now because using this app it’s been spot on about my cycle, and now with having no period I show nothing for my ovulation days or any futuristic periods. My period last month was also off and only like a day and half. I’m so confused - and if it’s too soon to tell, idk how the medication will affect pregnancy but if I’m not I don’t want to miss my chance at trying again.