Sounds to me like you're taking her out too often.
My boy Tyson has peed/pooped on me 3 times. Each time he did that he had been out for over 40 minutes. I no longer keep him out longer than 30 minutes and it hasn't happened since. (I should also note: all 3 times I was wearing a Red Sox sweatshirt, so maybe he hates the Red Sox??? Hahaha, just kidding, I just found that to be a funny coincidence. )
I would limit handling sessions to no more than once per day plus give her a day off here and there and see if that helps.