The article doesn't really try to hide it:
Without moderators or fancy algorithms, they are prone to anarchy
Anarchy?! I thought anarchy involved Mad Max style gunfights and burning oil barrels. What does "anarchy" mean in the context of a bunch of words on a web page? Oh, right, uncontrolled and uncensored discussion where people can say what they think.
Too often they devolve into racist, misogynistic maelstroms where the loudest, most offensive, and stupidest opinions get pushed to the top
So they don't like their comments (whereas they presumably did before) because over time the comments have become "stupid", "offensive" and - of course - racist/misogynistic/hate speech/bigoted.
I'm willing to bet that many of the comments that enraged them the most weren't particularly stupid or even racist, but rather belonged to a part of the political spectrum that Vice's writers wished they could make go away for real. If there's one thing 2016 shows it's the unlimited capacity for people to paint political views that they don't share of any kind, regardless of reasonableness or validity, as "racist" or "bigoted".