My Illogical Theory
'Cos Game Freak intended for it to happen.
But think - all Pokemon that know Guillotine have either claws, or something sharp like a blade. Mawile has jaws. It's like how we have jaws - we don't eat people in order to decapitate them - it's just like Mawile.
Also, this is Mawile's Pokedex entry in Sapphire:
Mawhile's [sic] huge jaws are actually steel horns that have been transformed.
So, in the end, they're not even jaws. They're horns. You can't decapitate someone with horns unless your just skilled at it.
Even though it may not make a lot of sense, in the end Game Freak just didn't want it to happen. So that kind of ends the story.
Hope I helped. :)