But even if the Jedi knew that the army was meant to be used against them (as far as they know, the army was ordered under a false name (Syfo-Dias was dead by then) by someone named Tyrannus, who hired a bounty hunter.... who happens to work for Dooku as well... coincidence?), as far as they know, they are lucky that they found the army and they can use it. Whether they bothered to investigate who ordered the army or not is not important: they found it, and they can use it. And of course , Yoda is not happy about that, but he had no other choice. The Jedi were outnumbered and needed help. He had to make a choice... and chose poorly... right?