Question Animation assets not getting into bundles?

I don't know the specifics that might be happening with Animations.

But one sentence you wrote sticks out "I have never had to explicitly mark these animations as being part of this bundle, in fact, they are shared with other character asset bundles, so should not be."

Normally with AssetBundles if something is shared by Assets in different Bundles then you must assign explicitly to a bundle. Otherwise it gets duplicated into each bundle. Some features of Unity, including Animation can be broken if an object that is expected to only exist once is duplicated multiple times.

I also found these internal notes about Animation and Asset Bundles. Its not describing exactly the same thing as your question, but might be helpful:

"When putting Animation objects into AssetBundles any duplication of the clips can break Assets like the AnimationOverrideController. The simplest solution is to make sure all the animation Assets are included together in the same AssetBundle.

But it also should be possible to split Animation assets into different Assetbundles, so long as they are all built at the same time and all the Assets are explicitly assigned to an AssetBundle. This is important because like all other Asset times, any implicit reference from multiple AssetBundle is resolved by embedding the referenced object directly in each bundle, e.g. duplicating them. That can lead to clips being duplicated and hence break the behaviour of the AnimationOverrideController.
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