Are you able to create steps to reproduce and post them to https://github.com/WordPress/gutenberg? I’m not sure why Gutenberg would be affecting admin-ajax.php, but if you can post some reproducible steps we can definitely try to fix this up for you (if Gutenberg is the cause)!
Hi there! I’m tofumatt, I’m a developer working on Gutenberg. Just so you know the HTML comments are saved in the database as the way to save block information, but they are not actually output on your site. At least when I just tested a site with the Twenty Seventeen theme I didn’t see the HTML comments in the output/frontend of my site 🙂