A lot goes into this and no one has it figured out and few can even relate to it well as most don't try.
The article posted above is great.
A few things to consider:
Boys will naturally get better as they mature and usually will get faster even if they don't work that hard. Girls who are maturing kind of get stuck, if they don't work hard, they clearly won't get better, but even if they do work hard they may not get better as fast as they want to.
Puberty hits some girls really bad and those may not ever be able to get back to the performances they had before that. I believe that number is a minority though. I believe a lot will certainly go through a plateau or slight regression period which in my experience covers 1 track and 1 xc season roughly. Just depends on which one is first. In my coaching experience this most often starts at some point during sophomore year in HS. The tricky part about this, especially with girls who are committed and have been successful is they don't like regression, so mentally it can be very hard to get through. On top of that for me as a male coach it's not something you really talk to the girls about. Occasionally parents will bring it up and you can have a conversation with them and it probably gets passed on. But a majority of the girls that I have coached who stay committed and patient will usually bounce out of this phase middle of junior year and can achieve better performances at the end of HS. Then there are some that it won't effect much at all.
This is the best answer (along with Lauren's well-written article). If girls stay diligent and patient while they go through the physical and emotional changes of puberty, they can and often do come out better and stronger in the end. Looking at the elite women runners, the vast majority are healthy looking, strong women who have clearly gone through puberty and (gasp!) even given birth!
The teammates that said that to the freshman are jerks.