Flushing Water Mains for Sediment

I saw this article talking about how the town Jackson MI was going to flush the water mains for iron and sediment. The water is still safe to drink, but could be discolored, and people are recommended to not wash their clothes with it. Since I study water, I was interested in the need to flush the pipes, sediment should be filtered out in the treatment system. Any thoughts? How did the sediment get in there?