There could be two reasons for it. First there may be one of the precursors in the the mixture with Fe nano particles. Secondly different peaks show different crystallographic planes present in the sample. So there is a possibility that your sample of nano particles has more that one type of particles. In order to look into detail of this try to take different samples for TEM and see is there any other crystal plan. I hope it may work
You can sustract the contribution coming from the unwanted phase if you have a diffractogram of them. If dont have it..well, do you really need to subtract them? The peaks ate already identified? Consider it is also information.