Buttons you've created most recently are in front and may obscure and take precedence over other buttons. Use the Bring Closer and Send Farther commands in the Objects menu to change their order. Background buttons are always behind card buttons. Press the Command and Option keys to see hidden buttons.
(Background buttons have thicker borders.)
Holding down the Shift key while you drag rounded rectangle buttons constrains them to the standard Macintosh button height.
Use a resource editor such as ResEdit to add or modify icon buttons.