There was no screenshot attached to this post, but I was able to reproduce the behavior that you described.
On my 2.3 system I created two named groups, both containing the same peak (Peak 1 in this example). After reprocessing and saving my results, the compound results table on my short ESTD report looked like the below screenshot:
As you described, Peak 1 is being reported twice now that it is a member of two different groups.
To resolve this, you can edit the table properties and select the option to 'Remove Duplicate Peak(s)' in the Peaks and Repeating properties:
After making this edit to my template, Peak 1 is only being reported once in the compound results table:
Hopefully this helps.
This is right, I'll update the same in my report template..