Yes, the pipes can have considerable iron buildup in them. There are a few ways to deal with this. Cleaing the pipes with Bleach, which I dont recommend since it makes the iron more permanent and less likely to release into the water, but with clean soft water, it will return. The other way is to ignore it, as long as your water coming out of the treatment equipment is good, the iron will lessen over time. Or a simple acid cleaning of the pipes with a safe mild acid. White Vinegar is commonly used since it is safer than other acids that if accidentally ingested due to dead legs in the plumbing etc, it may taste bad, but at least you know it is food grade. A solution of Vinegar flushed through the plumbing, similar to how you would clean a tankless water heater should suffice. My old house had red water for a very long time after the softener was installed. The water was great coming out of the softener, but the old pipes had so much build up on them that it was over 6 months of use before the water started to run clear.