This is a pass layer in Carrara, that usually renders as a separate image (I'm not sure whether it can be embeded or not). 

When you prepare your individual frames for combining in Photoshop, get rid of the fringe first, then add it as a layer for the gif animation. This way your layers in photoshop won't be dragging confusing maps around.

If you just want to alter the existing GIF, you will need a mask for every layer to consistently get rid of all the fringe.

Also, how are you aligning your layers in Photoshop?