Running Xubuntu Vivid 15.04 With panel placed at bottom of screen, using any app located within the indicator plugin it's menu covers the panel rather than appear just above the panel. If space reserved for borders is enabled the indicator menu appears properly above the panel. (Currently testing the intellihide panel hide, so that option is unavailable) If panel is at screen top - then indicator menu appears correctly regardless.
This happens because the the indicator applet now uses Gtk3 indicators. In gtk3, the menu placement code has been rewritten in gdk. It now follows the struts and _NET_WORKAREA_GEOMETRY more closely. This X atom is used to inform all applications which areas of the display are covered by panels. gdk will attempt to stop menus from overlapping these areas, and the window manager will attempt to keep fullscreen windows from overlapping these areas (those would appear behind panels, menus in front.) So clearly the autohide panel should not squash fullscreen windows. It should appear above them. But that means when the panel unhides, it can't set a strut. And that means gdk3 will draw menus on top of it. Gtk2 continues to not do this though, for reasons I don't understand. So this appears to be a regression in Gdk3, which is also the cause of https://bugzilla.xfce.org/show_bug.cgi?id=10625
I experience this bug with panel 4.12.0, indicator plugin 2.3.3 and Gtk3-bin 3.18.9 on Xubuntu 16.04. The problem started in 14.04. Here is the associated bug report from Feb 2015 -- same time +flocculant opened this bug: https://bugs.launchpad.net/ubuntu/+source/xfce4-indicator-plugin/+bug/1416843