It might not just be for award tickets. I know that this thread is about UA, but it might also explain what I saw recently when I purchased a SJC-LAX-MIA-SJU round-trip, which AA was offering for a remarkable $123 round-trip.

The outbound SJC-LAX flight had a nine-hour layover before the LAX-MIA red-eye, in spite of their being a later SJC-LAX flight that would require a much shorter three-hour layover. I assumed that the cheapo seats were gone on that later SJC-LAX. But then I saw a similarly priced routing with the later SJC-LAX flight -- but it required an overnight at LAX before continuing on to MIA the next morning. When I forced the computer to combine that later SJC-LAX with the LAX-MIA red-eye, the price went way up!

To the layman (me), it appears that AA is publishing a very low price but charging much extra for the most-desirable flights with the shortest connections. There might be some truth to that, but it could be as findark explained, and the computer didn't apply the married segment logic to the flights with a longer connection but also didn't break the fare.