Brown discharge followed by watery period.

Hello, Im new here and I have read through alot of posts regarding brown discharge. But I wanted to tell you my story specifically.

Firstly Im 24 and married. I dont use birth control or any other medications. However one time I had missed my period for 3 months. I took a pregnancy test and it was negative. I went to the doctor and he prescribed me with 10 hormone pills. He said to take 10 and by the end of 10 I would get my period. Sure enough, 9 days in, I got it.

However, the next time I got my period, it was brownish in the beginning for a good 5 days! Followed by a 7 day period. It was annoying. And now this month, the brown discharge began again, for 5 days followed by blood. The blood was normal for the first few days but now it is dark and watery.

Also this is gonna be probably the 12th day since the brown discharge began.

I have really minor cramps, not severe. and it seems the pattern of how the blood comes out is irregular. Some days alot, the next day minimal, and the next day alot again.

What is wrong with me? Is it a side effect from the pills I took?
Or is it because I had missed my period for 3 months and the lining in the uterus is still shedding?

Please help, I am becoming worried =|

-Thanks