Hi there,
You could use Admin audit reports to find users added to groups but that would leave out users added to groups more that 6 months ago (or 15 months if you used the API) so this would not be reliable.
The only real option is to export a list of users in the domain (or use the API to get a list) and then, if feasible (if you don't have hundreds of groups), export the list of users from each group (or use the API to get a list). Then you can use a spreadsheet to work the data and find which users from the domain match the list of users in any group. And which ones don't (which is what you want).
Hope this helps.
Best regards,
Nuno
Cloud Guardians
I strongly suspect you can do this with the free, open source, command-line, indispensable GAM tool. Check out https://github.com/jay0lee/GAM/wiki, https://github.com/taers232c/GAMADV-XTD3/wiki, and https://groups.google.com/forum/#!forum/google-apps-manager for more details. (I'd ask on that Google Group about the best way to do so.)
Hope that helps,
Ian