He said "GUM is in US, so you should put the flight coming into GUM".
At the GUM-HNL boarding gate, you are talking to an immigration guy. At HNL, you're dealing with a customs guy (there is no US customs on Guam, in general).
In general, GE processes you for both. However, GE GUM is really just about immigration, so the immigration guy is right, I suppose.
Regardless, USCBP has your whole itinerary (past and future) due to APIS. The airline does not know you're GE when it transmits your itin/ticket. GE is just grabbing the info from APIS.
But my question to you: Did the GUM GE machine ask you anything about customs declaration? Did you fill out the blue form and turn in to the HNL customs guy?