I run Antergos with MATE 1.16 and GTK 3.20 and have this same problem. I 
managed to fix it with the following change to indicator.py:
--- indicator.py.old    2016-11-22 09:32:35.572057252 +0200
+++ indicator.py        2016-11-22 09:32:48.745402358 +0200
@@ -316,8 +316,8 @@
         self.status_icon = None
         self.visible = True
 
-        def pos(menu, icon):
-            return Gtk.StatusIcon.position_menu(self.menu, icon)
+        def pos(menu, x, y, icon):
+            return Gtk.StatusIcon.position_menu(self.menu, x, y, icon)
 
         def right_click_event(icon, button, time):
             self.menu.popup(None, None, pos, self.status_icon, 0, time)

Maybe the x and y arguments where made mandatory recently?

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https://bugs.launchpad.net/bugs/1598298

Title:
  Variety menu shows up in left corner, instead of under the icon

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