I would try a second application of the vinegar to make sure that all of the minerals have been removed from the spot. The edges of the spots maybe starting to etch, which is why the vinegar did not totaly remove them. Try a very mild abrasive like 3M SMR to remove the edges of the spots.
Try to wipe any water off of your car as soon as you can to prevent
water spots. Once they dry on the finish, they can be a major PIA to remove.