I have seen refurbished machines missing screws although never on the outside of the case. Maybe if the machine had been in for repairs before and one of the screws wasn't installed/properly. To install RAM on the MacBook the screws do not come out of their sockets, but rather just loosen up -- and they are inside the battery compartment.
That may be an issue or sign of someone opening up the machine and thus voiding its warranty completely. You can either say nothing about that and hope they don't notice it or otherwise tell them the truth, and that it was second-hand and you honestly have no idea. It is ultimately up to them as they would have no reason to trust you, but you could also try a few times and potentially get a different genius.
The top case on the MacBook is covered under warranty if it gets the cracks/splits from the small bumps on the bezel above the screen as sometimes when closing hard or enough times they can break the top case at it's bottom edge to the right or left of the trackpad. If the crack/split matches up near enough with one of those bumps then it should be a clear sign for the genius.
However, as the others said, normal physical damage is not covered other than that design flaw.