My counselor has actually sent several of my letters of recommendation to a school that somewhat clearly states they don’t want them. Is this an issue that I should address directly with the university, or will worst case scenario (my counselor has said this previously) the university just throw out the additional materials resulting in no negative impact for my application?
Nothing to worry about. They will ignore any letters they don’t want to read.
Extra letters hurt when they come from ‘bigwigs’ who don’t really know the applicant, thereby implying that the applicant thinks they deserve special treatment because of their connections.
I would not communicate with the university. I would give your counselor a list of which recommendations you want to have go to which schools, and ask if they can please follow it going forward.