Depends on what is considered wrong
Estimates per standard practice have always been from center of fitting / structure to center of fitting / structure. LF always measured the total length of pipe from the start, to the end based on stationing. IMO civil 3d is listing the wrong lengths as the total don't won't match the stationing.
Technically though... you are correct, but in 20 years I've not seen a quantity excluded footage for every fitting.
Disconnecting the part might work. Trying to find a feasible way to use pressure pipe for water design in urban areas.
Mind letting me know what you're having your clients do MJ?