When you delete a file from the Incident details Action bar, the file delete command is sent to all of the clients that are visible in the Incident graph (whether or not those endpoints were selected in the Delete File from Endpoint dialog box). The file you intended to delete is deleted. However, it is deleted from all endpoints and not just the ones selected. If the file does not exist on an endpoint, then the extra commands show as in-progress in the Action Manager.
As a workaround, delete files from the Incident graph on the Incident details page or from the File details page.