While building many LEGO sets I have noticed that for internal pieces you cannot see when the set is finished; LEGO often chooses mis-matching colors. For instance in the (amazing) Saturn 5 set most of the pieces are of the white, black, gray family. However there are some green/blue internal pieces. Doesn't match the rocket at all. I have noticed the same thing with other sets as well where a random green internal pieces will show up.
Do they do this for a reason? Are they using colors that don't sell well and trying to get rid of them? Going for contrast to help you build?