I have had items seemingly duplicate on several occasions now, but without actually "creating" a new item. Instead, it seems like there is still just one item, but that it is displayed twice, and anything done to one of them also happens to the other.
Several times, this happened with magazines that I put into yellow protective cases. Loading the one from the backpack into the weapon would also remove the copy from the case.
One time, a friend swapped his damaged sewing kit for a pristine one he found, but when I followed his route later, I found both a pristine one and his damaged one, took the pristine one and in doing so, removed the kit from his inventory altogether.
I have over time also "lost" several items, which just disappeared from my inventory. This could be the same bug.