I've definitely noticed some instances like that too, but yes, it's probably where US feels they can fill up their planes without having to match fares.
One place I often see this is ROA-LAX when booking in advance. Fares on UA and DL for late February are around $300 RT, while US is about double that. They probably don't expect to have any trouble filling their hub-LAX flights between OD traffic and all the available connections, so they see no reason to fare match.
Sad for me though, since I'd like to lock in the ~$300 fares but I'd also rather connect through CLT and have a chance at an upgrade on US.