An Adam Le Fondre header provided consolation to two goals from the visitors' Lewis Buxton and Gsry Madine on Tuesday night, both set up by former Miller Chris Sedgwick.
But boss Scott now takes his team to a six day training camp in Portugal in decent shape.
He explained to the Star: “It was a real tough test, up against a strong, powerful side, but we stuck at it and I think our fitness is good at the stage we are at.
“I am disappointed with the two set-piece goals we conceded, we made too many enforced errors and there were some sloppy passes. But we have a lot of new players, it is early days, we are changing things and it will take time.
“But we’ll get there and we showed we have potential. Fitness wise, they are working ever so hard and perhaps one or two looked a little bit ‘leggy’.
“We have been working on our shape and we’ll keep working.”
Millers: Logan (Warrington ht); Marshall (Tonge 55), Brown, Cresswell, Smith; Schofield, Foster (Evans ht), Taylor, Pringle (Harrison 59); Le Fondre (Denton 85), Holroyd (Grabban 59). Unused: Annerson, Bradley, Gaughan, Hall.
Owls: Weaver; Buxton, Jones, Johnson, Bennett; Sedgwick, Prutton, Semedo (O’Connor 76), Johnson; Madine, Morrison (Amond ht).Unused: O’Donnell, Reynolds, Beevers.
Crowd: 5,589 (3,310 away)