Dear Luca,
Maybe you are mixing some databases or methods? The calculation for secondary materials for the background data sets only works inside the EN15804 add-on published in Nexus and only with the impact methods that are inside this database.
In cases where you are adding own foreground processes with secondary materials or in cases where you import other data sets with secondary materials, you need to insert the "Secondary materials (SM)" elementary flow by yourself to these processes with the correct amounts which will act as a "counter" (inventory indicator).
Best,
Conrad