In Episode 2, Obi-Wan Kenobi talked to Jango Fett on Kamino. Jango was clearly working under whoever hired/commissioned the clone army. Not minding that Jango told him that he was hired by Darth Tyrannus, he tracked Jango straight to the Separatist base planet where he is clearly seen working for Count Dooku and the Separatists.
Maybe Obi-Wan could have figured that as a bounty hunter, Jango had no loyalty, and had no trouble working for both the mysterious people who ordered the clone army and also Count Dooku — a conflict of interest that a mercenary probably would be able to handle.
But wasn't Obi-Wan a bit suspicious at all that the entire conflict was staged? Is this addressed in the Clone Wars series? The Jedi seem to be perfectly happy fighting the real war without any suspicions that the war was a manufactured and orchestrated diversion.