The stage manager as authority to note the show is something that needs to be established form the get go. It is artistic conversation that needs to start right away, with the stage manager establishing his or herself as part of the artistic team. Many directors/artistic directors don't trust the stage manager to give artistic notes because they stage manager has not an artistic bone in their body, no directing experience, or, throughout the process, didn't express an artistic thought or seem to be on the side of the artistic team in the process. Now, I don't know what happened in this particular process, but if the stage manager either didn't or wasn't allowed to establish themselves as an artistic authority for the show, it will be nearly impossible for the stage manager to give notes effectively. (This is also a problem when a SM takes over a show.)
My advice is to try to give notes as questions first . . . engage in conversation about artistic. (This helped me a lot as younger stage manager . . . dealing with actors much older then me.)
If the note is about new business added in a scene . . . let us say a bit about a actor playing with a hat that is upstaging another actor.
SM: Do you have a minute? I wanted to talked to you about the first scene, how do you think it went today?
A: Good.
SM: Was the hat business new?
A: Oh, you noticed it. Yeah, I was trying something new.
SM: How did it work for you?
A: (Now usually, when I call an actor on a new piece of business they will admit that it was a bad idea and offer to stop, but for argument's sake . . . ) I thought it was really funny.
SM: It was, but it is upstaging Cathy with her scene Derek.
A: Do you think?
SM: I think so. Why don't we cut back on the hat business, and let Cathy and Derek play their scene as directed, I just don't want the focus to become too split.
Usually at this point, the Actor realizes they were caught and will let the show go on.
Now, if they are really fighting for the hat moment, I will contact the director, sometimes brilliant discoveries are one after opening - I know, shocking - and I am not one to belittle the rehearsal process, but it happens.
In this particular case, with the Artistic Director not much caring either, perhaps this theatre does not see it as the stage manager's job to artistically maintain the show. (At my theatre, a major regional theatre, we have resident Assistant Director's who maintain the show.) If that is the case, and they don't expect or want you to maintain it, then don't fight it. Enjoy less responsibility.