Andy Keogh and Ian Morris were on international duty with the Republic of Ireland U-21 side, while centre-back Steve Foster was suspended.
Clubs are obliged to play at least six of the 11 players who have played in the League the most this season, with Scunthorpe naming just three.
United must pay £3,000 now plus £1,500 in a year's time.
League Two side Hartlepool United have also been fined, they must pay £1,500 - suspended for a year - after also failing to name six of their most regular players in the side.