Usually folks do the lightest color first, the darker color(s) over that. It sounds like the darker color is the one that got screwed up, so just redo the darker color. If you can do it without masking, fine, otherwise go ahead and mask and reapply. Having to add additional coats is a common problem if the last coat is not good enough. Usually the darker color covers well, so one tends to put on a very thin dark coat, and it is so easy to sand through. In fact, in order to eliminate orange peel one must often sand through to the point where what you observe happens. BTW, 400 grit is too aggressive, I never use anything stronger than 600, often finer, over any paint I hope to salvage.