I was in girl scouts, some time ago though, but in looking back we had transitional friendships I guess you'd call them. There were some activities that we'd all feel more comfortable and good at than others and we would just click with eachother based on our interests I guess you'd say. So we'd be tight one month and not the next.
If it's something serious though, and you have some pull in the group, I'd do something where I'd pair up the two girls that aren't getting along and have an activity that centered around trust and depending on eachother, but a fun activity. Like, take a bandana, cover one girl's eyes and have the other direct the other girl. Call it a scavanger hunt or something. I'm sure you could do better, lol, this is my 30 sec. idea. But maybe there's a map and one girl has to tell the blindfolded girl to walk 6 paces her left, right, etc.
Without knowing more, the girls may be in different peer groups, guy issues, maybe the parents aren't even getting along or a teacher favors one student...who knows. It's always nicer when things work themselves out naturally. If it gets bad, I might mention something to both girls parents but in a way where I'm not favoring one girl over the other, just that I noticed some friction between the girls and ask both parents if they have any insight.