R.D.
If her tummy AND bottom hurt, maybe she's trying to pass hard stools, and it hurts to poop, so she's holding it, which in turn is hurting her belly. Maybe give her something to soften stuff up, lots of fiber, maybe a little prune juice.
The bottom alone could mean maybe she's not getting wiped properly... not your fault, 2 1/2 year olds are wiggly! Have her bend over and touch her toes... if she's a little rashy, wipe well with warm soapy water on a wash cloth, then put a little Desitin on there.
My best guess is the first thing though.