There are a lot of different scenarios that can lead to multiple animation layers, but typically it will have to do with a pose having been created and saved with animation layer data which then translates back into the scene when applied later unless you specifically tell it not to. There are a number of different ways to get your animation down to a single layer, but the simplest, IMO, is to just save it as an animated pose. If there are layers active when saving a pose, it will ask if you want to keep them separate or collapse them into one. Once you've saved it collapsed, you should then be able, in either a new scene or in the original one after deleting the animation layers, to apply your newly created pose. Since it would have been saved with the multi layer data collapsed, voila! No more layers.

Just one of many ways to skin this cat. :) -Les