Just watched the commentary track and found out that the midichlorian test scene and Anakin asking where Padma is were both added in later. They really stick out as Jake Lloyd is a lot older and the lighting does not seem as good.
They also said that Darth Maul hitting the laser generator beam with his lightsaber was added in later. However, that is one of my favorite scenes in the movie, and is very on brand for Darth Maul.