When windows are grouped, the tab bar added above the windows' titlebar pushes the windows down. If the windows' height is maximized, this pushes the bottom of the windows offscreen (if the taskbar is set to hide, or is somewhere other than the bottom of the screen) or below the taskbar (if it is visible in its default location).
This is particularly a problem with program UIs that make use of all the vertical space available. If I want to group Adobe Creative Cloud programs, I have to manually size the window or else lose access to a row and a half of buttons. In such cases, Groupy is more of a hassle than a help.
Solution: Grouped windows' height should be automatically reduced by the height of Groupy's tab bar, at least for windows with maximized height.