Father of a freshman girl
Unfortunately what they are saying is probably true for a vast number of high school girls. While boys go through significant growth spurts and dramatic running improvements if trained properly, girls will go through puberty related changes that will likely increase their weight and change their shape in ways that will make them slow or plateau in their running times. On top of that, girls are much more likely to have iron deficiencies that will slow them down too.
Here's a good read for you and your daughter:
Best thing to do is be supportive, patient and persistent. And do a lot of research or find out from others on how to train, eat, rest, supplement and set expectations accordingly.
I have a freshman daughter who has had a lot of success in running for the past couple years and we will be facing the same challenges.