Here is copy and paste from DNR online license sales.....was the guy one of the exceptions for special license, disabled, or land owner? Otherwise I don't see why anyone would not have the habitat fee paid. I don't even think there is a check box online for habitat fee when purchasing.
#030 OUTDOOR COMBO LICENSE (1 Year Hunting, Fishing and Habitat Fee) - Iowa residents 16 years and older, and nonresidents regardless of age, are required to have a valid Hunting License on their person, and have paid all applicable fees and possess all required stamps while hunting except for: landowners and their children hunting on their own land, hunters 15 years old or younger hunting with a licensed adult, and persons that qualify for special disability or income-related licenses. Iowa residents 16 years old or older are required to have a fishing license to fish or otherwise legally take, use, have possession of or transport species of fish from inland waters and boundary rivers of Iowa, as outlined by the regulations in the annual IA Fishing Seasons and Limits pamphlet. Additionally, the Habitat Fee is included, so one can hunt or trap anywhere in the state except for residents that have special licenses for the disabled or landowners and their children hunting on their own land.