There are no Economy Plus fares filed for CVG-MHT, so the itin is being constructed as a broken fare combination of CVG-EWR and EWR-MHT fares which do have Economy Plus fares. It's not that surprising that the broken fare would be more expensive than other types of through fares on the route. Even though UA website calls these "B" fares, they do not actually appear to be B booking class fares (unless they just book all Economy Plus fares into B booking class) . When I looked up the fare basis codes when I tried it, they were a combination WAA2OFIN and SAA2AFIN fares. The "I" in the second to last character of the fare basis code identifies it as an Economy Plus fare.

Delta uses similar "branded" fare products for it's Comfort Plus fares with underlying coach class fare basis codes. But it has dedicated W and S booking classes for their C+ fares (not to be confused with UA W and S classes which are just regular coach classes). There is a dual inventory check (there must be both inventory in both underlying coach fare basis class, as well as W or S booking class which the fare books into) when booking these fares. The dual inventory check helps fares from getting "upside down" (Main Cabin is more than E+/C+). However, dual inventory checking won't help when there are no E+/C+ fares filed on the through route and you need to book a broken fare in order to book E+/C+ seats on itin.