No one has ever referred to what BZ did as a plot-hole. Most just refer to it as an ass-pull and those saying so being primarily Madara fans or people who hate BZ.
At the end of the day, BZ was stated to be undetectable by everyone, even sensors. It's not problematic writing. It's just embarrassing for Madara fans. That's all. Madara bragged about everything and stated how he had been running the show all along, only for us to find out that he was just a toy for BZ just as Indra and the other vain Uchiha had been. Black Zetsu's reveal as far as his planning goes would be a retcon. Kishimoto rewrote the entire Uchiha clan story, portraying them in an even more negative, naive light than before. This opened some plot-holes, like how was BZ able to even read the tablet when he didn't have the ocular powers to do so? Why didn't anyone notice within that time? Why did Madara think BZ was his will, if BZ just popped out of nowhere one day and wasn't from him? Things of that nature.
As far as Yata and Totsuka go, I don't see the correlation. Those don't fall under the category of plot hole, deus ex machina, or ass-pull. Itachi having a technique isn't a bad thing. (By that logic, every single thing in the series is an ass-pull since people show new techs all the time.) As an audience, we know that he was very intelligent, a prodigy, and did research since he was a young boy when no one else cared or even wanted to. He'd be the most likely to have those weapons. People tend to complain when Itachi has trump cards... that holds no weight. It's just his fighting style. He's not one of those noob shinobis that uses his most powerful tech first- he starts off with kunai like a real ninja and works his way up. So, things like ending a battle with Tsukuyomi, Izanami, Susano'o, etc make perfect sense and aren't bad writing- they're actually nice additions. Plus, he's the character that has the most references to mythology via his arsenal. All his techs represented something with his character, they weren't just randomly added for power-ups like Kishimoto did with the other Uchiha and characters.