Cough:scanner:cough shows stains, scratches, and water spots far more clearly than an enlarger. I don't know why but it does. I had one like that but printed just fine on my enlarger.
What I usually do is to soak my film in weak acid (like stop bath) to losen the calcium content of the stain, then soak long time in filtere/distilled water. Then rinse, photoflo, and dry. It usually works.
I wouldn't scrub it with alcohol as you have a chance of scratching the film. Even if it is on back side of film, it can show. I've done it.