I had the issue with the ears and the mouth as well. Randomizing the nose and, thus, eventually being able to select a nose color made the game re-add the color to all body parts.
On PC it is like that, so maybe it's also applicable to console: You click on the nose. Then CAS shows you the several options of nose types you have in form of a list. This list shows up inside of a framed window which is headlined as „nose“. In the right corner of the window at height of the headline should be a dice symbol. When you click on the dice the game randomizes the specific features, in this case the nose. I needed to randomize the noses twice, because the first time around the colors showed up again but the list of colors you can pick from was weirdly overlapping with the selection of the nose types, meaning the layout was corrupted. Otherwise you can randomize the nose once, switch to a different body part and then back to the nose, since after „closing“ the framed window and opening it again the game should sort the layout out by itself.
