YC doesn't operate YC companies. They're investors. They aren't your boss. They're not looking at your code. They're almost certainly not doing any meaningful technical due diligence. These are things that happen, to an extent, in priced rounds that happpen after your seed round (A-round technical due diligence is also a joke, but whatever, stipulate). The whole point of YC is that they're investing in big batches of startups, at a scale that is a big multiple of what an A-round VC does in a whole year.
Tan is apparently apologizing because he spoke up on behalf of a batch company, or repeated some misinformation TechCrunch published. But it is very weird to ask them how their selection process would change to account for this happening.