This is a common type of joke. A person will say, "What? You mean..." and then pretend to be surprised by something. For example, a woman might say to her boyfriend:
What? You mean you'd rather stay home and watch football than go shopping with me?
This type of joke makes the most sense when the thing that you pretend to be surprised about is something obvious. In the example at top, no one wants to stay at work all night. So it's clear that the speaker isn't really surprised that people want to go home.
You can also use "What? You mean ___?" seriously, when someone says something that surprises you:
What? You mean you're not coming with us?