In front of the Sky Sports cameras at a sunny Glanford Park, McCall's men lost out in an entertaining five-goal encounter thanks to Matt Crooks' late headed winner for the hosts.
It could easily have been City who grabbed the game's decisive goal, however, with Timothee Dieng, Rory McArdle and James Meredith all going close before Crooks' intervention.
Dieng's chance in particular looked a promising one for City but the goal-bound header hit Scunthorpe 'keeper Luke Daniels on the shoulder.
City laid siege to the Scunthorpe goal during six minutes of injury time at the end of the game, with Romain Vincelot hitting the bar and Charlie Wyke and Daniel Devine also threatening.
Meredith arguably had the greatest chance to snatch a late leveller but his close range header was somehow deflected over the bar via the outstretched boot of the grounded Murray Wallace.
McCall said: "To be honest, we would have been slightly disappointed to have only come away with a draw from this game. I think our second half showing merited the victory.
"We perhaps didn't play great in the first half but came in at the break ahead thanks to two good goals.
"After the break, we played with real quality and desire, and we created a number of scoring chances.
"How we've not scored in that second period is partially down to just bad luck. We've hit the bar, had a effort hit the 'keeper's shoulder and an effort hit their defender's knee and bounce over.
"We could have done better ourselves with some of our finishing but three or four of those moments in the second half were down to just pure bad luck.
"The goals we have conceded have been sloppy as well though, especially the two from set-pieces.
"The ball is on the money from the corner for their winning goal, and Crooks is a big lad, but there were things we could have done better and that we will address.
"The end result is clearly a disappointing one but we can take plenty of positives from the performance.
"I think the supporters could see the effort the lads had put in.
"We've twice responded in a positive fashion after conceding early in each half but football is about winning, and we've not won.
"You get games like we've had today (Sunday) in football sometimes, it is how we bounce back now.
"We've got six games to go in the league. If we keep putting in performances like we did in the second period, we'll go from strength to strength."
City were without Nathaniel Knight-Percival at Glanford Park after the defender suffered a nasty cut to his face during training on Friday.
Josh Cullen was also unavailable, the midfielder watching on from the stands after playing for Ireland U21s the day before.
In Knight-Percival's absence, Kevin Toner was handed his City debut, with the Irish defender netting his first senior goal during the opening period.
Toner was named in a back three, as McCall elected to also play the recalled Billy Clarke just behind the attacking trio of Mark Marshall, Alex Jones and Charlie Wyke.
McCall added: "Along with his goal, I thought Kevin's overall performance was good.
"He showed good quality with his left foot and he attacked the ball well. I think he suits playing in a back three.
"You have to be adaptable and flexible as a coach and a player, and we had two formations we could have gone with today.
"I don't think this game was won and lost due to tactics though, it was more because of our sloppiness for their goals and some poor finishing and bad luck at the other end."