How could Makoto Shishio break Sanosuke's futae no kiwami?
Well as it was stated in the anime and manga, Shishio has the unique ability to neutralize any and all techniques he's seen before. So having witnessed Monk Anji multiple times over the course of his servitude use the many variations of the Futae No Kiwami, it would stand to reason he knew how to counter the technique.