With the Tigers leading 2-0, Wilks won his side a second spot-kick of the afternoon but refused to hand the ball over to designated penalty taker Josh Magennis - who had already notched from 12 yards in the first half.
Skipper Lewie Coyle eventually stepped in and took the ball off the former Leeds United forward, only to then find himself on the receiving end of a shove from the 22-year-old.
At that point, Magennis opted to let Wilks take responsibility for the penalty, which was successfully converted to wrap up a much-needed victory on the road.
And post-match, City head coach McCann insisted that what went on had been quickly resolved and was no big deal.
"You've got two forwards who are desperate to score goals, they're hungry for goals the both of them," he said.
"They're best mates are Josh and Mallik, after the game there in the changing room they were hugging and dancing with each other.
"In the emotion of a game, people want to score goals. Mallik's obviously thinking 'I've made a really good run here, I've won this penalty, I should take it'.
"Everybody knows Josh is the penalty-taker, but look, Mallik's taken the penalty, he's slotted it away well, there won't be a big deal made out of it. It's done and dusted. It's over.
"Mallik has scored. Josh has spoken to Mallik. We've all spoken together in the changing room. It's over and we've won the game."
Asked about Wilks' shove on his captain, McCann added: "Yeah, but it's nothing. Mallik is that type of guy. He lives on the edge, I think that's what makes him dangerous and makes him what he's about as a type of person.
"We've got a good group here and Mallik is one of those lads who is really highly thought of within the group.
"These things happen all the time on the training ground, it just so happens that it's in a game today. You draw a line under it, you speak to the players, you forget about it and you move on.
"It's done. I've had a chat with both of them there and both of them are hugging each other and kissing each other."
It was Magennis who drew first blood from the spot on 24 minutes, firing the ball down the middle of the goal after Keane Lewis-Potter was shoved inside the box.
The lead was doubled shortly before the interval when Magennis headed on Coyle's right-wing centre and Reece Burke was perfectly placed apply a finishing touch.
The points were then wrapped up in controversial fashion in the 64th minute, Wilks winning his team a second spot-kick of the afternoon having cut infield off the right, before clashing with Magennis and skipper Coyle over who should take it.
Having eventually won that argument, City's top-scorer calmly beat Dons custodian Sam Walker to make it 3-0 and move the Tigers to within a point of second-placed Lincoln in the League One standings.
And McCann was pleased with the control his players demonstrated during what he said he felt would always be a really difficult encounter.
"From the outside looking in people will look at this game and automatically think Hull should go here and win easily - but it's not the case," the Northern Irishman added.
"This team is fighting for their life at the bottom end of the league, it was always going to be difficult. But, we focused on making sure we got our own house in order.
"The shape of the team was excellent, we were calm on the ball, we were controlled and it was nice to see three goals go in again away from home. I'm pleased with that and another clean-sheet.
"We were really good and disciplined out of possession and we had to be. We had to be good defensively and I thought we were. But then when we went forward we looked really exciting and like we could score goals."