How is that a plothole? At the most it's something not entirely explained (yet).
But it's rather easy to guess. All Zetsu, including Black Zetsu, were created through the use of the Gedo Mazou, which is the remains of the Shinju. Since we know Kaguya has some connection to the Shinju, it's really not that far fetched to think she was present in the Mazo as well.
Also, remember that, while Madara used Hashirama's DNA in the creation of his articficial huamns, the result were no exact Hashirama clones, but the Zetsus, which are originally the product of the Shinju when Mugen Tsukuyomi is used. So, Kaguya's influence was definitely at work there.