Since the print is lighter in the problems areas the negative should be darker in those respective areas. Can you see anything when looking at the negative on a good light box? If so I would suggest a stain or hard water buildup of some form. Touching layers on a reel, water spots ahead of development, etc. always result in a 'thinner" negative in such a problem area.
Did you put the film in the tank for a while before souping it? If some moisture was in the tank, it could have affected the film prior to developing. I got some weird results on a roll of negs when I put the film in the spiral, dropped it in the tank, and then never ran the soup through the tank for about a week.