No, this is not a connectivity issue. This is actually an attribute issue with the naming convention of the PCF file.
To show how this could happen, let's say you create a new project. You go to modify your Relationship Instances in Project Administrator ..
You decide: "I don't need Unit. I don't use it". So, you delete it.
Later on in the project, you have completed all your pipe runs and you want to run Isogen. Then this issue happens. You may have failed to notice, however, that Isogen will prompt you for the PCF naming convention. It calls it "connection criteria" but this is also used to name the PCF file (and the iso drawing). Notice the default settings below:
Even if you change the Naming Rule; UNIT is still shown under the Criteria Fields. If it's not removed, AutoPLANT will assume there is a unique value for each component (actually it's a NULL value) and will split all components out onto separate iso's.
The solution? Check your Criteria fields and ensure that all fields are actually valid. It's an easy one to miss.