As he fled the store, he tried to grab the baby, but couldn't get her loose from the stroller straps. When he began carrying it out, Easterly, as she had learned in a training course, shot the man once in his knee.
If he was carrying the baby anywhere near his chest, the leg shot would probably have been the safest one (for the baby) she could have taken. Perhaps her training course emphasized taking the safest shot to stop the perpetrator. I imagine, if he was pushing the stroller out the door in a normal fashion, she would have aimed higher but that's just an assumption.