Periods twice in a month. Right?

Hello. First I'll share some pre required information - I have a tendency to gain weight due to which my periods get delayed by a few days. I had intercourse ( using protection) on 13th March. I checked for pregnancy after 10-12 days - it was negative. Now, I got my periods in 29th March ( regular flow) and then 29th April. I gained weight and my periods were delayed in the month of May. After 29th April I got my periods on 5th June. And yesterday evening,  surprisingly, i had them again!! It's just spotting as of now.. so I'm not sure if it is actually a period or no. The blood is brown in color. I had started exercising a week back so could it be because of that? Or is it because of something else. It couldn't be because of pregnancy, right? Because I had my periods regularly for 3 months and I eat a lot of papaya and other related foods.