Cysts & Clomid

So, I took my first round of Clomid in Dec. I ended up getting a cyst on my ovary. The dr gave me another 50mg dose of Clomid this month (Jan).... I just finished my last pill yesterday and I have side aches that feel like the side ache you would get if you had gone running. Could that be from the cyst? I get the pain from just simply walking. It's not enough to put me over the edge but still enough to be uncomfortable! Has anyone else gotten cysts from Clomid?