If you are confident there has been mistreatment, I would discuss this with her.
However, I'd be wary that since you have no evidence to show her she will just deny it, minimise what happened and try and get your partner on her side...which he already seems inclined to be anyway so he's unlikely to back you up.
It might be that the best thing you can do is to get your partner to tell her you'll no longer need her to watch your child anymore as it's no longer necessary. And she no longer gets to babysit either of your children - though she doesn't need to be told that.
This will be difficult to manage without your partner on side, and the most important thing is that she's no longer alone with your children.
To be honest I'd be hugely tempted to confront her about what you've been told myself, but with no partner on side, no evidence to show her, and not having witnessed it yourself, it would only go one way....basically her denying it and getting in her son's ear that you're paranoid, believing some random stranger over her, your child was being difficult and that's all the person saw, etc etc.
The best thing you can do is just stop her having your children alone from now.