Hi,
Thank you, after some extra reading of few threads I found out that I needed to change this:
remove_filter('the_excerpt', 'wpautop');
to this:
remove_filter('the_content', 'wpautop');
in my functions.php
Although still the solution needs to be a bit more clear as the issue occurs even in the default WP themes in a completely fresh installation. Ideally it should be fixed as it also causes a lot of issues with other editors, for example SiteOrigin ones and Advanced TinyMCE.
Thanks,
Olga