Same issue here. Changing the GTK theme (in this case, I’m using breeze-gtk) during a session yields the correct titlebar button size (minimize, maximize, close).
However, logging off and logging back in results in huge buttons. Note that the button icons are actually wrong as well (e.g., the x should be inside a circle).
Update: I was able to resolve this problem (i.e., the icons maintaining correct size after logout) by installing the breeze-gtk theme through the official repos and NOT the “Get New GNOME/GTK Application Styles” button.