The "you guys" instance seems a bit silly at first but is a good example of the way our language promotes the idea of male as the default. Note that there are no feminine words which we gender-neutralize in a similar way--we refer to a collective as "guys" or humanity as "mankind," but never use "gals" or "womankind" to refer to a mixed-gender group. In this way we construct women as an other, in opposition to men: the expected members of the workplace are guys, we expect history-makers to be men, and women are the odd exception to that rule.

It is important to note that very few of the people who use these linguistic constructs are being intentionally sexist in doing so, and as such nobody is taking hurt or offense away from the use of "guys" to refer to a mixed-gender group or anything like that. This is not an exercise in respecting others' sensitivities so much as an effort to recognize the way our actions subtly reinforce the problematic and undoubtedly biased power structures that exist in our current culture. As others have pointed out in this thread, the participants in Hacker School share a common interest refusing to reinforce said power structures, and as such put rules in place to codify that commitment to helping one another change the way they interact with the world.

As others have noted, these are not accusations--which would certainly not be appropriate or productive to whip out in the middle of a meeting--but gentle reminders amongst like-minded people to watch the way their words impact the world around them.