happens all the time. on both Y and C searches.

sometimes there are segments that are married, and if one of the segments is very full, sometimes it wont show either even though the other is totally valid to get you to the destination and bookable over the phone. as for non-stops, i'm not sure why. but both these usually happen on HUB-HUB connections (small city destinations usually always show up).

this is why its important as a UA veteran to memorize all flights from your home city, and know the best connections for HUB-HUB destinations.