Thank you very much!
The duplicates were the reason!
The orphan elements/element groups that will be disconnected from flow are on purpose.
But I still have a question regarding to the over constrained and edge-spanning elements. What are the disadvantages of these? Though I could easily fix them using FUDAA PrePro, I only observe that if I have many over constrained elements, the simulation in parallel mode will not work, but as long as I use the normal one (without parallel), the simulation goes fine.