Little late weighing in.
I would keep a very close eye on him the next few times you're there to be completely sure the other mother's behavior really is baseless. If she has a point, you need to deal with your son. If you don't see anything, I would complain to the gym.
I think that other mother is handling her dislike (which, again, may or may not be warranted) for your son in a very immature way. Perhaps she's afraid to confront you not knowing if you'd be nice about what she has to say. I don't know...
Still, you can be the better person and not let it turn into a confrontation. Clearly, she doesn't feel comfortable talking to you so don't force her.
And maybe even if you don't see the rough behavior she sees, you might talk to him about watching out for and protecting children smaller than him.
As far as that other mother goes, I'd give her a wide berth. She's not handling things from her end very maturely. You don't need people like that in your universe.
By the way, with an age range like that gym has -- is there not a separate place for the pre-walkers to play away from the bigger kids? If I had my baby playing somewhere that I constantly felt he/she was in danger of being hurt by other children who are playing, I'd find another place for my baby to play! Maybe the gym needs to consider that before a child DOES get hurt...