The Clone Army plot sort of came up when Obi-wan was looking for the assassin hired to kill Senator Amidala. It wasn't what he was looking for, so he didn't focus on it. He got some information, let the Council know, then continued on his mission, hoping that he might get answers from Fett, but with all the business leaders making a deal with Count Dooku causing Obi-wan to be distracted even more from him mission, captured, and the Jedi (plus Skywalker and Amidala going in against the wishes of the Council/Republic), all that got lost as the war started. The Jedi/Republic deciding to just accept the Clone Army that has for some reason been created for them by a Jedi that has been dead for a decade, with no motive sensed by the Jedi, and use it against this very obvious massive combined Droid Army threat. The Jedi, I suppose, guessed everything was the will of the Force since things fell into place for them, and just went with it, not knowing about the Sith plot. Dooku's talk with Obi-wan wouldn't get to the ears of the Council until after the Battle of Geonosis. Even then, I am not sure they classified Count Dooku as a Sith Lord until later in the war. And then, via the Clone Wars, mistakenly thought that Dooku and Maul were the Sith Lords until near the end. Only then did they start to figure out there was still the Sith Lord Dooku had mentioned was controlling the Senate all those year ago. By then it was far too late, and the Jedi had all but lost. All that was needed was an excuse for Palpatine to have them exterminated and have the public praise him for it.