When it comes to thumbnails: it is possible that you are using multiple thumbnails on your site, while watermarked is only the default one. Please check that.
There is a way to remove watermark, but you’d need to do the following:
1. Do not apply watermark to full size images
2. Install any plugin that allows regenerating images (for e.g. AJAX Thumbnail Rebuild or Regenerate Thumbnails). Both allow you to regenerate images using an original (full size) image.
3. Then, if your original (full size) image doesn’t have a watermark applied to it you may regenerete other image sizes and so remove watermark.