You are right, group nodes cannot be resized using the width/height properties. I filed a corresponding bug report in our internal issue tracking system.
That said, it is nonetheless possible to resize groups interactively. To do so, select the group and drag one of its resize handles. (Resize handles are the eight small squares around selected nodes.) Note, that you cannot reduce a group's size below the size required to hold its content (+its insets).
If enlarging group nodes does indeed not work for you, maybe resetting yEd to its factory defaults will help. To do that delete the contents of yEd's profile directory. If that does not help either, please tell us which version of yEd (the latest version as of this writing is 3.9.2), which Java version (see "Help -> About"), and which operating system you are using.