Yeah, theoretically after Bane, only two Sith existed at the same time. The odd thing is that the rule was created to conceal the Sith from the Jedi. Yoda therefore should not know about it. Lucas might have stuck that tidbit in for the fans, but in doing so he messed with his own history.

In The MagFan edit of TPM, he modified that scene so Yoda says, "there are only always two- no less." Before, he said, "there are always two, no more, no less." This fixes that continuity error.

And then, if we really want to be confused, we can look at all the apprentices, from Vader's in the new SW game, to the numerous Sith found in SW novels and stories. We can only assume that after the Sith took back the galaxy in RotS, they decided that the rule of two was no longer necessary.

Yoda Is Your Father said:

Seems to me that the Republic/Jedi were in the business of 'purging' threats... maybe the Sith deseved their revenge.

Yeah, they seem to have done a lot of that. Probably got a bit paranoid after the first conflicts. As much as this was derived from the bad dialogue of the prequels, maybe Anakin wasn't so far from the truth when he said the Jedi had grown arrogant. (Or whoever said it. I feel like a bad fan at the moment.)