From my limited experience in Livebearer Breeding (I traded in my Tropical Community for an African Cichlid community months ago), here's what I've learned:
With Mollies - the male is usually more agressive, especially if you have other males in the tank. If you have a single male with two females, and you're finding that the male picks on one female more often, it could be because he doesn't have enough "women" that are interested in mating, so he's singled out one and going after the only one he can "get any" from. My best advice would be to add at least 1 or 2 more females for that single male. Most stores will tell you that you have to keep a solid ratio of 1 Male and 2 Females, but in my experience, I've found it works best if you have 3-4 Females for every Male.
Of course, you'll want to make sure that you have enough room in your tank for a few more fish, and that the tanks are of adequate size for Mollies. Because of their active nature, I've seen articles that recommend a 20-Gallon as the absolute smallest tank for a school of Mollies. Anything less than that may cause some undue stress amongst the community. I can't say if this is true or not because I've not kept Mollies in anything less than 30 Gallons. Someone else may want to advise you on this one.
Is this part of their mating process? Thanks in advance! 
