Because Arkay protects the souls of humans from soul trapping to lead them to the afterlife. Black Soul gems are a necromancer invention to work around Arkay protection.
Arkay protects both man and mer.
But yeah, it would make sense if there was some lore around Arkay breaking this convent, ever, for any man or mer, there just isn't though.
To make matters worse, even if arkay revoked his protection of the falmer, they should still all be grand souls, but they are not, you can get lesser and common souls from falmer.