I just finished running Morwitijaal and nabbed the FD Sword, but when I went to look I had 2 of them. I remember looking in my inventory a bit after Itnamzand and had two Noble Swords as well. I thought the Noble Sword was a fluke and that something else had one for some reason.
I don't think I have two versions of RoH running, as I only have one ESP on. Not sure what's up as I've never run through these until today nor have I reinstalled the mod to make duplicates as far as I know.
I'll keep an eye out on other duplicate things, but so far it's only been these two. I hadn't gotten a duplicate Ocarina of Time because I had this installed since 5.0 core and got the Ocarina then.