Turns out GNOME Tweaks caused this. I restored default settings in GNOME Tweaks, then I logged out, and in a tty, I reinstalled ubuntu-session and every part of the yaru theme:
sudo apt purge ubuntu-session yaru-theme-gnome-shell yaru-theme-gtk yaru-theme-icon yaru-theme-sound sudo apt install ubuntu-session yaru-theme-gnome-shell yaru-theme-gtk yaru-theme-icon yaru-theme-sound
then after logging in, all the themes were applied correctly.
Turns out GNOME Tweaks caused this. I restored default settings in GNOME Tweaks, then I logged out, and in a tty, I reinstalled ubuntu-session and every part of the yaru theme:
sudo apt purge ubuntu-session yaru-theme- gnome-shell yaru-theme-gtk yaru-theme-icon yaru-theme-sound gnome-shell yaru-theme-gtk yaru-theme-icon yaru-theme-sound
sudo apt install ubuntu-session yaru-theme-
then after logging in, all the themes were applied correctly.