Whisker Menu aligned with button rather than panel can cause it to overlap double row panels
Setup a double row panel, and check the option to 'Use a single panel row' Whisker Menu Panel Button (under Whisker Menu settings Appearance tab). In this case, if the Whisker Menu button is on the bottom row of a horizontal panel, the Whisker Menu will overlap the panel when opened. Probably this should be considered a low priority enhancement request, but it would be much tidier looking if the menu aligned with the panel, rather than with the button, such that it doesn't overlap the panel when opened.