I’m seeing the same warnings, over a thousand of them each day, since the upgrade to 5.3. I’d really like to know which files WordPress is trying to chmod() in my user’s home directory, but the warning doesn’t say — and I don’t get a stack trace, so I don’t know if this is a legit piece of WordPress trying to change permissions across a thousand files, or if this is some misbehaving piece of code that I should uninstall that’s calling class-wp-filesystem-direct.php::chmod()