Schools expect you to have chosen your recommenders with sufficient confidence that you do not need to see your recommendations. I doubt that admissions committees look at a file and say, "oops, didn't release his letters, he's out!" On the other hand, it might plant a grain of doubt in the reviewer's mind.

I think you're correct in not wanting to draw attention to it at this stage. However, if you get an interview and there is an opening, for example if you are asked about a supervisor, you might slip in the fact that you did not recognize the implications. As far as factors affecting admissions go, this one is not at the top of the list.