Content Aware Fill Aborted

It sounds like your workflow is seriously flawed. 

You can't animate any of the transform properties of a layer that has Puppet Pin applied. The mesh is generated when you set the first pin and if the layer moves, the mesh doesn't. You have to Pre-compose.

Content-Aware Fill only works with Video. It will not work with still images, it requires a hole in the layer,  and it requires some fairly consistent pixels inside and outside of the hole you create with a mask or a track matte. If you are trying to fill in some kind of hole made in a layer when you apply CAF then you will need to pre-compose that layer and let CAF work on the hole.

If your image sequence is a is sequenced layers and the video arms are moving then Puppet Pin cannot be used to control the movement of the arms. The moving arms will foul that up.

If I had some arms that I wanted to move with Puppet Pin, the arms would be the only thing on the layer, nothing on the layer would move until I added puppet pin, and the background would be on a separate layer.

If I am misunderstanding your project then we need screenshots showing what you are trying to do on the layers. Select the layers, press the u key twice, then drag or embed the screenshot to the forum so we can understand what you are trying to do.