I've had this problem a lot - since I use KVS I can see available fare classes.

However what I have unfortunately found out is that a significant part of the time - most especially with connecting fares - there are actually 2 types of fare buckets on the same flight.

1 is for the direct city to city, the other is for a 'non-stop' through the connecting city.

Many times now I've been completely unable to book what appears to be available on individual legs, but not when put together (i.e. joining the individual legs and thus removing the double taxes and other UA friction costs).

Really annoying but there you go.

Sometimes I have been able to book these fares via Orbitz or Expedia though!