He took the wrong positioning on the war in Ukraine. Along with others.
And it looks here like he made a series of personal relationship mistakes.
The man can't speak for himself anymore, but it's not a good look and I don't think his partner has done him any favours here by deflecting responsibility.
Clearly awful mistakes were made.
It is entirely in line with Chomsky's historical pattern that Epstein could walk up to him, say "the US government hates me and claims I'm a pedophile" and for Chomsky to then treat him like his best friend. It is also worth noting that when he eventually recanted his Cambodian genocide denial, he basically said something along the lines of "how could anyone have possibly known just how bad the regime was?" which is... essentially what this response is attempting to be, "how could we have possibly known that Epstein was actually a pedophile?"
There has been never part of interesting intellectual debate between him and anyone who has different opinion. He writes to his followers.
Any tyrant or autocrat who opposes America is somehow not that bad. For example: The Cambodian Genocide by Khmer Rouge in 1970s were exaggerated by "Western propaganda", The Srebrenica Massacre, some killings but not genocide.
Russia. He argues that the U.S. "provoked" Russia by expanding NATO eastward. Russian attack against Ukraine was American fault. In his logic superpower like Russia should having a "neutral" buffer zone is a legitimate security concern. Smaller European countries can't have their own sovereignty. They must be either US puppets or part of reasonable Russian sphere of influence. At the time he is against US sphere of influence in the South America.
You must also have noticed that he never engages his critics honestly. He just dismisses them as "elite propaganda".
Noam Chomsky, the man who has spent years analyzing propaganda, is himself a propagandist. Whatever one thinks of Chomsky in general, whatever one thinks of his theories of media manipulation and the mechanisms of state power, Chomsky's work with regard to Cambodia has been marred by omissions, dubious statistics, and, in some cases, outright misrepresentations. On top of this, Chomsky continues to deny that he was wrong about Cambodia. He responds to criticisms by misrepresenting his own positions, misrepresenting his critics' positions, and describing his detractors as morally lower than "neo-Nazis and neo-Stalinists."
From the intro of a lengthy examination of Chomsky on Cambodia: https://www.mekong.net/cambodia/chomsky.htm