Sifo-Dyas IS a plot-hole in that it's never properly explained in the films. It's left as a vague puzzle. "Sifo-Dyas ordered the clones...Sifo-Dyas died around the same time...Tyranus hired Jango to be the template for the clones." That's it.
The natural conclusion is that Sifo-Dyas was impersonated by Sidious or Dooku, so they really should've left it as 'Sido-Dyas' and not had an actual Sifo-Dyas at all. George told us it'd all be explained in Episode III, but, uh, it wasn't.
Then the EU overcomplicated things by making Sifo actually have a premonition of war, and rather than tell the Council and all, he goes to Dooku and confides...Dooku, already being wooed by Sidious. So Dooku helps him order the clones, then kills him to become a Sith, but oh wait not really, he keeps him alive in stasis to use him to aid Grievous' transition to his cyborg body!
I love the EU, but sometimes it's just dumb.
It was explained in the labyrinth of evil, and its not a plot hole. Don't see how it is since its made very clear that, he ordered the clone army without the authorization of the council but was killed before that and Palpatine used his name to make the army. Its not that hard to understand.