When setting Chromium or Firefox to not use the system title bar and borders / hide title bar, somehow the breeze theme is used for the button theme. I think I remember it using the right theme on XFCE, so it should not be an issue with chromium or firefox.

Here is chromium with system title bar enabled:

And here is chromium with system title bar disabled:

In System Settings -> Appearance -> Application Style -> Gnome/GTK Application Style, did you set both GTK2 and GTK3 to an explicit different style?