I would be careful to discern between fraud and police state allegations of fraud. Aaron Swartz is clearly the latter and it at least deserves to be mentioned in the article.
I agree that Y Combinator is good at filtering out fraud - and I'd argue that's why they have so many high value companies - which would invalidate your argument that these balance out. Why do you think they're good at filtering and why do you think the effects balance out?
Summary
I estimate that 1-2% of $100M+ YCombinator-backed companies have faced serious allegations of fraud.
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I would like to thank Oli Habryka for pointing me to about half of these examples.
Addendum: Founder Fraud
I additionally came across 2 founders of YCombinator-backed companies who were charged with fraud unrelated to their business:
In this list YCombinator publishes of their most valuable companies, the one closest to the bottom that I can find a public valuation estimate for is Fampay, ranked #311, with a valuation of $150-170M. I think the difference in valuation between companies at the bottom of this list is relatively small, for example Drchrono (#269) was acquired for $180M. Additionally, there are 13 publicly traded YCombinator companies with a market capitalization above $100 million. So I’m going to guess that there are around 400 companies with a $100M+ valuation, but I’m not sure.
I can’t find information about their valuation, but they raised $3 million at their most recent round and I would expect that this was in exchange for a 20-50% stake
Using the same 20-50% heuristic as with Stablegains, applied to their $4.2 million series A
Same heuristic, applied to their $10.8 million series A
They have not raised outside the initial YCombinator investment, which generally values companies at $1.8 million
Standard heuristic, applied to their $56.4 million series A