When you are trying to do synchronization connector and splice are replaced from schematic, But the wires will be added and the existing wires will not be deleted because there may be a chance for , This will cause packing of two wires in single cavity in a connector because of existing wires may have different attributes with schematic wires.
To avoid this While doing the synchronization you have to delete the existing wire in the harness before starting synch process.
Find the below image for your reference.
Doing synch without deleting existing wires,
Doing synch after deleting the existing wires,