If a photo or video file in a Motion project shows checkered rectangles throughout the bounding box, the file is offline. This can happen if you updated your iPhoto or Aperture libraries to Photos for OS X.
To show the media file, open iPhoto or Aperture. Then open the app library that contains the photo or video file. Opening the library brings the media file back online so it appears in the Motion project.
Finally, save the Motion project and collect all the project media into a folder so the Motion project has a unique copy of the photo or video.