When you have a BOM with different alternate BOM's (alternate number) then the system use the following filter sequence:
"From the list of iterations filtered previously (View + BOM Type), the system should try to match exactly the Alternate BOM entered in Configurable Structure. If none, then the system should use the lowest in the hierarchy defined in a configuration file; as the OOTB Alternate values are alphanumeric, the lowest one should be the first ordered value. If no iteration matches, then the system should try to get the one with "Null" as Alternate. If the user hasnt entered any value, then the system must match the "Null" value."
The result is: when you filter on a specific alternate number and for a WTPart/BOM, this alternate number does not exist, Windchill choose another alternate number.
See my example (ATS = alternate number 001) and BEU (alternate number 002). If you put a filter on the structure, you do not want to see another alternate bom but the default manufacturing view if the alternate number does not exist.