If your Instant Articles are missing images that show up in your regular articles it's probably for one of the following reasons:
Featured images cannot be repeated in the article body The plugin intelligently parses the article body and removes the featured image if it is found to be repeated.
Images cannot be duplicate Images in the article body cannot appear more than once. If an image is found to be repeated the plugin will remove all but the first instance.
Additional the plugin checks that all images are available and don't 404. If any do they to are removed.
For more information see the official Facebook blog post on images here.