I have a horrible feeling this is going to be a difficult one to fix.
From any MATE Tweak option which uses the Brisk menu (say Netbook) there are two right-mouse-button options against an application, Pin to Favourites Menu and Pin to Desktop. There is no option to Pin to Panel; a workaround is to pin to the desktop then drag the icon from there to the panel. (With Netbook, pinning to the panel would be the most obvious action).
Similarly, options which use Plank (say Pantheon) have no options available from Plank to preserve the icons elsewhere. Dragging the icon to the desktop or to the panel results in it disappearing in a puff of smoke.
(Ironically, Traditional gets it right).
I presume this is because Brisk and Plank are third-party applications and the integration with MATE is incomplete.