Throughout the lunar scenes, the Earth is gibbous, despite the fact that it's just before sunrise hence the Earth should be "new". It's only in the final scene with the Monolith, where the rays of the rising sun strike it, that the Earth is shown in its correct phase. (Bowman has only been on the Moon a few hours; it would take the Earth about ten days to go from gibbous to new, as it takes the Moon here on Earth.)