Pompey, the pre-season favourites for promotion, have so far managed just one win at Fratton Park while losing to Oxford, Chesterfield and Saturday's opponents Fleetwood.
Town's winner had a touch of fortune about if after Jamille Matt's shot was well saved by John Sullivan only for the ball to bounce off Sonny Bradley and into the net.
Nevertheless, Whittingham is expecting a big improvement in upcoming home games against Rochdale, Bury and Wycombe.
He said: "We've had players sent off in two of those games and then conceded because of a ricochet in the other.
"We've now played the top three teams here, but we've got some good home games coming up and we've got a good chance of winning them."