Before upgrading I had a couple of template overrides inside a custom theme as stated here:
https://developer.matomo.org/guides/theming#twig-the-template-engine

After the 3.9.1 upgrade, the templates are no longer being loaded.
I have manually reverted this section in my installation
https://github.com/matomo-org/matomo/pull/14051/files#diff-55e7eb22dafce9c6bf9d3fc98022f2ebL547
and the overrides started working again.

After a few var_dumps I found out that the new code just loops across all folders and doesn't consider the theme folder to search there.

Aside from the custom theme generated by the console that only overrides colors and a adds a couple of static html to some visualization templates, the installation is clean.