When Auggie and Jin argue at the kitchen table, Auggie empties her glass. A few sentences later Auggie takes another sip from her glass which is half full again without anyone refilling it.
The Staircase Project plans to accelerate something to the San Ti by exploding bombs behind it to provide acceleration. No way to get the bombs in place ahead of the craft they will propel.
If the technology that aliens built took them a million years, how is it that their planet in a 3-sun system survived all these years? The only explanation is that their planet was much further away in orbit and slowly moved closer. That was never fully explained.