The root logical connection is using a leaf system port instead of a root system port.
Improvements made to the logical connections require that the root logical connection be associated with ports of root systems and not leaf systems. The logical connection in error still has a relationship to a leaf system instead of a root system.
The database may not have been migrated properly.
Updates to the associated structure will put the logical connection onto the To Do List. If the structure is detailed, the assembly and physical connections will fail to be created.
What You Should Do
Open the model.
Run the Clean Database custom command to fix the connections with this error.