It's the external shots that are the goof. We see the windows face directly outward when the shuttle is flying in space, but when it approaches the moon, the windows now face to the side (the shuttle's rockets are pointed down, and yet the crew can still look out and see the moon. They should have only been able to see empty space).
Not entirely sure what you mean, but there are two sets of windows. The cockpit windows are pointed "up" (relative to a landed position) so the crew would be on their back when they landed, and the passenger windows are pointed outward around the "waistband" of the ship, so passengers will be sitting upright when landed.
If you meant that the cockpit crew could see the moon's surface when they were about to land, then yeah, that would be a goof.