It may help to post a screenshot of the layers panel and or describe the layer structure. A screenshot of the action panel with all steps fully expanded could also be good. Do all of the files contain the same layer structure and names? Can you process the same files using the action outside of the Batch command?
It may be for several reasons. Image mode must support layers and another reason can be that none of layers is selected. Each step in action is independent, can be executed on its own but many steps has some requirements like Duplicate layer, for example, which has requirement that some layer is seleted in the layers panel.