I think it would have been a good idea to have taken her to the doctor when she was in this much pain, the doctor will know what to ask and what to look for. She could also be looking for some attention too, since she is no longer the baby, especially at the age.

Another thing to keep in mind, just because someone has been abused as a child, does not mean they are abusers when they grow up, in fact more aren't than are.

And keep in mind this child could be "playing " you all, one way to get attention is through negative actions and anything that will put one parent against another.

I have 3 step kids who are adults now, but when the oldest was 13, she made up a whole bunch of stuff that was happening on the weekend when she was with us, and instead of her mother asking us about it, she would just get on the phone and yell at my DH for stuff he never did.

I also had a daycare and child at the age are prone to make up stuff, I had one child (8) who was in my daycare because her nanny she had for years, died. So she would go home and tell her mom that I wasn't feeding her lunch and stuff. They are old enough to know what to say sometimes to cause trouble. But you also need to always be careful when a child is hurt, it could even be her brother she is fighting with, or a neighborhood kid, or someone at school.
As far as not wanting to go home, when she is with you both, do you have a lot of fun and plan things around her? My DH was "disney dad" at first, until the kids expected that dad revolved around only them. Having step kids and kids in broken marriages, are tough , no doubt. Keep your eyes open and if she complains like that when she is with you, don't hesitate to get her checked out. Good luck