I've just started using Spine (great software package!), and I'm seeing these same warnings with the latest unity runtime (the one dated 4/25).
Animator is not playing an AnimatorController
UnityEngine.Animator:get_layerCount(Animator)
Spine.Unity.MecanimTranslator:Apply(Skeleton) (at Assets/ImportedPackages/Spine/spine-unity/Components/SkeletonAnimator.cs:180)
Spine.Unity.SkeletonAnimator:Update() (at Assets/ImportedPackages/Spine/spine-unity/Components/SkeletonAnimator.cs:82)
They don't happen all the time, but every now and then I'll do something in the editor that tickles this and causes these to appear when I make any changes to the scene. If I run the game and then drop back into edit mode, they go away for a while, but they always seem to come back.