If you want to leave a comment about a lemma, definition, remark, etc, please click through to the page of the lemma, definition, remark, etc and then leave a comment. Only leave a comment on a section if your comment is about the whole section or about text which is not in any environment, e.g., it is about the introduction to the section. This should be pretty rare.
If you have a longish comment involving mathematics and especially latex code, it is helpful to send a copy of your comment to the email address for the Stacks project (stacks.project..at..gmail.com). This will make it much faster for me to incorporate your suggested changes.
Technologically advanced people can use github and do a pull request.
Finally, if you don’t want to comment in public, then you can email the stacks project at the address mentioned above. Of course, I will be the one dealing with your email, since I am currently the maintainer of the project. So you could also decide to email to my personal email address. But if you do so, then there is a chance that I will overlook your email due to the large volume of incoming email in my personal email account. So I strongly prefer emails addressing issues with the Stacks project to be sent to the Stacks project email address.
Thanks for all your comments!