Agreed with everyone else here :>
From my personal experience, I don't think that the filly would be pregnant (though it is possible, but i've never known a horse in my travels to get preggie as a yearling) but at the same time ANYTHING can happen with horses.
I would get the foal aborted for the sole fact that she will not grow correctly. Think of it this way... Would you ride a 300 pound 13 hh yearling? Well, that yearling will be carrying the weight of a foal around 24/7, so it will be as if she had a rider on her for about 8 months (I would say 12/11, but i'm factoring for the baby to grow inside, obviously it isnt as heavy as a rider the day its concieved).
And as everyone else said, chances are you'll lose both. If you don't lose the mother during child birth, her knees and joints and insides will be so royally messed up that the humane thing to do would be put her down.
It sounds to me that she got into a TERRITORIAL stallions pen, and got the crap beaten out of her. Joey is really territorial, and every time we introduce a new horse to him he beats the crap out of them, even if they don't run. So i think that Mr. Stud created a hole in his fence, and the baby passed through not knowing that he didnt want company.
Personally, I will never, ever, ever keep a stallion in a neighboring pasture to some mares unless i want babies and fence renovation, lol! (I'm saying this based on a 4 - 5 ft high Equine fence). If nature calls, he will answer it, even if it means jumping a fence.
Hope your filly turns out to be ok