1- If there ever was a scene with Yoda and Qui-Gon, why was it cut? Perhaps Liam Neeson didn't do the voice over and they cut it? If they did, the whole explanation of the Jedi spirits was not given to the audience!

2- Also, the explanation of why a Jedi disapear and some don't is not clear (perhaps if you know how to mantain your consciousness after death, you can also make yourself disapear).

3- How did the clones know about Order 66, and why did they obey? Hypnosis? They were all trained in kamino to do that? Didn't the Kamino cloners find weird that a Jedi went there to ask for clones that would eventually KILL the Jedis? Or maybe Sifo Dias was not the one there, but how about when Obi Wan was in Kamino?

4- And yes, the whole thing about the babies. Didn't Vader/Palpatine sense anything? Vader knew he would have a child, he never bothered to look for it in Tatooine? Perhaps while visiting his stepbrother, Owen Lars...? Or visiting his mother's grave, right NEXT to it?