Sometimes - like when a quarterback runs runs or a running back passes, even to score - the fantasy scoring will not be displayed in the Game Center simple box score.
All scoring is still counted in the final score.
To see a players full stats, select "Full Box Score" in the Game Center tab of the desktop site.
For the app, select any player to bring up their Player Card. From there, click the stats tab to see a full box score for each of their games. Make sure you scroll all the way across to see every category.