When you drew network B into the profile you no doubt chose to 'entire network' and therefore got all of the network except for the connecting structure, which is part of network A. Which is logical and correct. All you need to do now is to select the connecting structure, by itself, and have it drawn into the same profile.
A 'network' appears to be just an organizational unit to group chunks of a piping system into some rational arrangement based on your use and desire. (by road, branches, phases, whatever) The members of a network don't even need to be connected all together. The limit is that any one object, structure or pipe, can only belong to one network.