Okay yeah we played that wrong, we thought that the top score was the number needed to eradicate. Then other 2 were the scores 1st & 2nd place receive.
So if I understand correctly the points are awarded 1st-3rd.
The situation happened at the end of the game with only 3 cities left. Only 1 player was situated in the city with no one else able to get in. That player ended up filling the final spots on their last turn.
For whatever reason it took me several plays to get all of the rules right (at least I think I know them now...) but yeah, the top number is the City's Population to meet for it to be Eradicated but also it is the 1st place score. The 3rd place score is the one used for Death Toll scoring.