On the synthesis of nano-structural hydrogenated graphite by ball-milling under H-2 atmosphere, iron contamination was mingled from steel balls during ball-milling. It is clarified by spectroscopic measurements that the mingled iron formed a non-stoichiometric iron-carbon (Fe-C) compound. The Fe-C phase was transformed to a well-ordered phase with H-2 desorption at 450 degrees C, suggesting that the hydrogen atoms were anomalously trapped at the Fe-C phase. With respect to hydrogen absorbing properties, the mingled iron enhanced the hydrogen capacity by about 50% compared with iron free hydrogenated graphite, where H/Fe was about 13 mass%. Therefore, if the hydrogen absorption site originated in the Fe-C phase could be synthesized independently, it should be recognized as a promising hydrogen storage system.