I gifted three copies of a game but SGTools thinks I only gifted one. Help?

You'll have a better chance for a quick answer by posting directly in the sgtools tread: https://www.steamgifts.com/discussion/b736C/tool-sgtools-new-section-deals

Why would you care what SGT detects?
It does not influence your contribution value on SG.
Most SGT ratio checks go for a real CV ratio of 2 or lower, which you meet with those two copies missing.