Critical Research Failure: Returning with a vengeance, as Peter attempts to describe the three other anime series he crossed the Daria characters over with and makes many laughable errors in the process of "enlightening" the audience.
Riding Bean was not a prequel to Gunsmith Cats, but the pilot for a different series. They don't even share a continuity (and actually can't - Rally isn't even the same ethnicity in the other series!).
Nagisa in Koko Wa Greenwood doesn't run the yakuza. She does have a group of henchmen who do her bidding, but only in plans that involve humiliating her brother. This creates a bit of a problem as the plot of the fanfic requires that she be a maniacal murderous villain, when she's just not up to it in the series.
...it is very unlikely that a teenager from the late 90s in America would have seen or read Rose of Versailles considering that the manga was never released in English and the anime didn't get licensed until 2012. As fansubs were hard to come by if you weren't in college and had an anime club to hook you up, there's not a chance Daria heard of this to the point where she would immediately connect Shun's being raised female with Oscar's masculine upbringing.
Contrary to Peter's note pointlessly explaining the end of the Gunsmith Cats OVA, it was Rally who killed Natasha Radinov. Collins got a lucky shot in that broke the axe blade, but Rally guns her down at point blank range. Collins holding it over her head in the story (and Rally agreeing!) is a completely lark.
As noted in the MSTing, Peter makes a note that tempura is "stir fried fish in a wok", when it's actually batter dipped seafood or vegetables.
In the actual Koko Wa Greenwood, Shun is feminine in appearance and mannerisms, but only pulls the "bent gender" gag once as part of a hazing on Kazuya. Beyond that, he identifies as a heterosexual male and has no interest in actually being a woman. In the fanfic, Shun is a pre-op transgendered woman who has just gotten breast implants and also voices his love of men and his wish to get the rest of the surgery done so he can be a fully biological woman.
Ron the Death Eater: Nagisa goes from being a comically inept villain seeking nothing but the humiliation of her brother to murderous international crime lord with no explanation.