Difficult age IME, my DD is 10.6 now and I remember a couple of years ago to that just beginning to be a bitch age. Her and her friends would fall in and out of friendship constantly. As you describe, there was one girl who nobody seemed to like but always included.
What worked for my DD was to have a sleepover but with one other participant. Once you go above there just being two people in a situation, it is inevitable IME, that a clique will appear and one person is left out. So 2:1, 3:1, etc.

I am in a similar position to you, in that I too have a Y3 girl who is 'friends' with quite a manipulative little girl, who is also the daughter of one of my friends. It makes life quite awkward sometimes. I do try to encourage my dd to foster strong friendships other than with this girl, and I am here for her to talk to whenever she needs to vent. I think that helps enormously. I try not to get too personal and defensive whenever she speaks to me of this girl, instead I try to keep a neutral tone and try to help her to see the 'bigger picture' as to why this girl might behave in the way she does, while at the same time remaining sympathetic to dd.

It is a tricky path to navigate, but I wouldn't get involved in any but the most extreme of circs. I think your friend was possibly being faaaar too defensive herself in phoning you up and confronting you, perhaps if it was my dd I would have had a quiet, almost apologetic word with you and suggested that we work out a strategy to help get through this. But then I know I would be mortified if it was my dd who was being seen as a 'problem'.

I was a very sensitive child who went through mild bullying at school and as a result I am hyper aware of any problems that may affect dds, as I know how much it can affect your whole life. The only thing I do try not to do is 'project' my fears and personality onto my dds. They are actually quite different in many ways to me as a child, and I think dd1 is possibly a lot tougher than I was.

I think the best way is to stay out of their friendships. You can't affect what this child says and does but you can help your DD by helping her develop a confident and mature response to the behaviour. i.e. helping her know what to ignore and what to stand up against.

I've bought "Queen Bees" from Amazon (can't remember full title sorry) and it gives really good advice on how to advise children through friendship issues.

DD1 had a lot of hassle from a 'friend' like that (she was 5-6 at the time). We used to discuss what happened and how DD1 dealt with it is, and talked about alternative ways to deal with it. I helped DD1 to understand that such behavior is not nice, and that she didn't need to stand for it, and to call her friend on it (e.g. I don't want to play with you unless you stop (whatever bad behavior was going on at the time). Overtime, DD1 got quite assertive. They are no longer friends.

My dd now 8 had a similar problem with a girl in her year 2 class she controlled all the girls and told them exactly what they should do. She was unhappy so I told her to go and play with another of her friends and to make it know that the other girls could play but only by their rules this time. The rules where that no one person was allowed to be the boss and tell others what to do. If she didn't want to follow those rules then she couldn't play. Anyway the short story is that all the other girls in her class came and joined her group and the very bossy girl was left with one friend.

My dd has been happy ever since but she did take control of the situation.