This has more to do with reservac failures with complicated routings than married segment logic. Many ofnthe fares that are published are not available online and/or agents don't even know they exist.
Op, When you call in just ask them to make sure their "connection arrows" are on. They will know what this means. This will usually work for under 4 segments. anything more will require a more
Manual approach to searching (the Agents should also know this term as well) That's all I can say for now.
But yes, if ita is displaying a fare and you are compliant with all the fare rules (especially advance purchase requirement and watch for sales/ticketing restrictions) then they should be able to replicate the fare.