I read the situation and the responses given and would like to share that I have a very similar situation but it is my 3 year old grand daughter that does not like her mother.

They have a had a very volatile marriage and my daughter curses and tyraids so I have heard and I am sure she has seen and heard things she should not have to hear.

They separated and my daughter in law use to put my grand daughter on the phone and have to ask Daddy to come home. It was heart breaking. My son refuses to believe that she put her up to it. It is obvious because even when she gets on her play phone at my house the first thing she says is Daddy when are you come home?

Anyway they are back together and it seems that within the last few months my grand daughter's dislike to her mother has really grown. It has been slowly showing up and I have not paid that much attention to it but lately is getting very obvious.

Example: I was playing checkers in the backyard patio with my step grand daughter age 12 and my son sat down with us then my grand daughter sat down. Only 4 places at the table then my daughter in law came up to watch and my grand daughter age 3 said you don't have a place to sit. I didn't really pay attention until my daughter in law argued with her and said, yes I do, and made my step grand daughter move over to sit with her. My step grand daughter said no I will sit on a this stool nearby and seemed very irritated at her mother for even coming up to watch us play. We played for a while as her mother was reading a magazine and bringing up topics about people in the articles but we continued to play and all seemed fine. Then my daughter in law left and my step grand daughter took the seat back and what got my real attention was when my 3 year old grand daughter said good for you to my step grand daughter,you got Mommy's seat. And she said it twice. I looked at my son and I said, did I hear what I just thought I heard? Again I didn't really pay it attention until she said it again and then I stupidly reacted with surprise and said to my son, Did I hear what I think I heard? My son made a comment about how she can be but I didn't want to say anything more in front of her.

Later I could not stop thining about it and it brought back other situations that I had brushed aside. I don't want to make a big deal out and I know my grand daughter is really smart and I should not have said anything and she loves to tease which she learned from her mother but it just caught me by surprise. It seems excessive to have this kind of thinking at age 3 and really concerns me.

My son and daughter in law having their problems has been disruptive and hard on everyone in the family but seeing my grand daughter and step grand daughter in a sort of collusion like this also bothered me. I am trying not to over think it but it made feel something is definitely not right here and my instincts went into second gear later on. I love both of these children and felt very sad.

I don't know if there is a cause for concern or not, given the age differences between siblings. While it may be sad, I think that because they have a problem marriage, and maybe deal with it differently than you would like, that maybe the real cause of your concerns, and just me, I understand you being partial to your son, and its easy to see things that support that feeling, so be aware that grandparents may have concerns but should stay out of their children's business, because no way do we have all the facts, and are prejudiced for one side against the other.

Don't bother protesting, because that's the way it is with parents. The main thing is enjoy the grand kids, love and nurture, but never judge either parent, nor interfere in the issues between them. Observe from a far and get facts and not just feelings and that's hard to do for grandparents, but your grandchildren should never know your concerns.

Do pay close attention to them, but be wary of how much you see or hear from them, because like your own children, grand children can see, and deal with things on a different level that's not really fact based.

I wouldn't think that a 3year old could actually hate her mother. However due to the separation of her parents, and not having her father around in the every day routine, she probably felt that loss. Now that your son is back in her everyday routine, she may feel jealousy sharing his attention.
Its hard thing to have to sit back and watch this situation play out for you, how up setting it is. Its even harder for children to have live in the middle of it. But as a grandmother you can just reassure with your endless love and understanding. Volunteering to babysit for your grandchild will not only give your son and daughter in law grow up time to bond, but it also give you extra time to be with your grandchildren. I hope everything works out!