We got the "you're in!" email, and the whole team was pumped. Having to go back to them hours later to let them down was really hard to do.
The fact that Ycombinator sent the "oops, sorry!" email from a do-not-reply address and basically did nothing to make up for it showed a real lack of respect for the companies that were affected.
Will it make a difference in the long run? Probably not, no one wants to shoot themselves in the foot over what is basically just a disappointment. But it really does lower Ycombinator's brand for a lot of people. Not a great example to set.