That is unusual. I would recommend opening the hose bib on the bottom of the hot water tank and see how much debris you have in the bottom of it. I usually see considerable hardness flaking when a softener is installed, white flakes and chunks falling off the plumbing and clogging the aerators, not usually dark chunks unless it is on galvanized plumbing. In my old house, the water ran red for over 6 months after I installed my softener. The Galvanized plumbing was over 80 years old so this was not unexpected. Try bypassing the softener and see if any more stuff comes out just to make sure you do not have a damaged lower screen inside the softener.