Hello,
Do you mean that the alternative 0E does not exist ? If yes, then the function module CS_BOM_EXPL_MAT_V2 picks up the only alternative which is valid, if you make that single alternative in active, you will get zero rows.
I checked your case in my system and got the same result 
Then further, I created 2 alternatives 1 and 2, when 2 is made in active and passed as a parameter to the FM, it returns no entries as expected. However when only a single alternative exists and if you pass an alternative which does not exist, the FM picks up the only alternative which is valid.
I think, you can add a custom check, before calling the FM, of whether the alternative exists or not, from MAST table and not call the FM if the alternative is not there.
Hope this helps solve your query
Best Regards,
Ameya B.