Could be a lot of things, but this is something that happened to us, weirdest thing ever, it's called "sineulstesthia" or something like that.
My son woke up crying one morning screaming that his leg hurt (several months ago). It was 5am and I thought he had gotten out of bed to pee and maybe stepped on a toy. So I layed him down with me and he calmed down, we went to sleep. About 2 hours later he wakes up and is in extreme pain, limping, telling me how bad it hurts, in tears. I try to take him out to the living room and at this point he can't even sit up, says his back hurts, can't walk, I'm trying to wiggle his legs, check his range of motion, and it obviously hurts him. No marks, no bruises, no redness or swelling, I'm baffled. So I give a dose of Ibuprofen and wait for the doctor's office to open. He becomes increasingly less upset and starts to get comfy as the pain killers kick in.
Go to the doctor and by then of course he is fine, but after seeing him like that I just wanted the doctor to check him over and make sure he was okay. The cause we find out, is because this sinul-whatever it's called is a viral infection that attacks the joints and causes anywhere from mild to extreme pain from the inflammation it inflicts on the joints. It usually goes away as quickly as it comes on, and oftentimes presents with no prior symptoms of infection (fever, fatigue, etc). A dose of ibuprofen, the doc says, and he'll be surprised if it happens again, but if it should to give him a call.
Well it did happen one more time, about a week later, not quite as severe, and the doctor asked blood to be drawn just to ensure there were no auto immune issues presenting, and said they might have to take some x-rays to make sure no signs of juvenile arthritis were presenting either(and he is 5 yrs old and the doc says yep, that can happen). But another dose of ibuprofen and not another issue since. Viruses take time to work out of the body, typically 21 days to run their course, so the viral inflammation that caused the pain died off and now he is fine...
It was crazy, and I felt great knowing my kids doctor knew what in the world was going on. He said a lot of parents freak out and take the kids to the hospital thinking they broke a bone or something, just to get a dose of ibuprofen and sent home. Thank goodness for such a sharp doctor that knew the answer to his illness, because I was getting freaked out. But give her a dose of ibuprofen maybe and see if it continues.
She could have pulled a muscle too, fell and bumped her knee, (ever get one of those bruises thats like invisible but you hit that part of your body on something and all you know is its sore?)maybe even chipped a bone or something. No matter what, I'm pretty sure it will pass.