Confirmed on our site as well.
We were seeing Justified Gallery break only when Yoast SEO was active after updating WordPress 6.9.4 Galleries would stack incorrectly and lose their justified layout.
Adding the following to functions.php resolved it immediately:
add_filter( 'should_load_separate_core_block_assets', '__return_false' );
This appears to be related to the newer separate core block asset loading introduced in WordPress 6.9. Once we disabled separate block assets, Justified Gallery began working normally again even with Yoast enabled.
