When you create a new site, you can choose the HiDPI option for high resolution output. This causes, that all images are placed in half of their size in order to obtain an adequate resolution on high res monitors. If you scale these images to their original size, they don't meet the requirements of HiDPI any more and you get the upsample warning. You can control this behaviour in "site properties". Just look here:
Adobe Muse Help | Creating High Resolution websites
Edit: A look at your screenshots confirms, that you have switched on the HiDPI option: Behind the assets you can see the label "2x".