They don't have the resources for an investigation, they barely have the resources to fight this war. And if they don't use the clones - who I consider slaves - then millions will be subjugated and/or killed by the Separatists. I've yet to see a single *workable* suggestion for what the Jedi should have done differently with the army.
Not using the army would be insubordination or even treason, as they've been ordered by the chancellor to act as generals. So immediately the Jedi would lose their investigate mandate, making efforts to find out more about the clones not just immensely difficult but also illegal.
Meanwhile the Separatists are freely putting people in camps, enslaving entire species, occupying worlds without any effective opposing force standing against them.