Wilks won the Tigers a second penalty when his side were leading 2-0 at Plough Lane.
However, the ex-Leeds man refused to pass the ball to designated taker Josh Magennis – who'd already tucked home a spot-kick in the first half.
That led to Hull captain Lewie Coyle grabbing the ball off Wilks – before being shoved in the chest.
Magennis would then hand the ball back to Wilks, who converted to wrap up the three points.
Tigers boss Grant McCann played down the incident, however, as his side stayed third in League One.
He told the Yorkshire Post: ‘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.
‘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.’
Meanwhile, Michael Appleton insisted Lincoln's high-scoring defeat to Plymouth has to be a learning curve.
The Imps lost 4-3 at Home Park but remain second in the table.
Appleton said: ‘Our reaction to the way we started was good. The way we started the second half was excellent, outstanding. And then I’m disappointed not to take the game away from them at 3-2.
‘Then, again, at three apiece, we had the stronger chances. I’ve got real mixed emotions. It was a massive learning curve for one or two of the players in the team.
‘It’ll only be a learning curve if they actually learn from it.’
Darren Ferguson insisted Peterborough remain grounded despite stretching four-points clear at the summit of the table.
The Posh fought back to beat struggling Wigan 2-1, with star striker Jonson Clarke-Harris plundering a double.
Ferguson said: ‘Nothing is won in February and March. Our aim hasn’t changed since the start of the season and all I will say now is we are in a good place. We are not getting carried away. We are focussing on the next game now.
‘This was a fantastic win. We let ourselves get frustrated in the first-half when we were far too frantic. We were better in the second half, but when we conceded a fluke goal it looked like a tough game to win.
‘But credit my players as they found a way again. That’s seven games now when we have come from behind to win. To score twice in the last 10 minutes shows the character and attitude of the players and you need to that to be successful.’
Lee Johnson praised Sunderland’s comeback as they earned a draw at Crewe.
The Black Cats were 2-0 down at half-time before strikes from Jordan Jones and ex-Pompey forward Chris Maguire clinched the away side a draw.
Johnson said: ‘It's a wonderful point won by two bits of individual brilliance," Johnson said.
‘Both of those goals you'd expect to be in the top ten goals of the season.
‘We needed it because in the first half, it was tough to watch. I can't give you an answer why, whether it's the number of games back to back, maybe I've got to look at myself and say, was this the one to make five or six changes?
‘What upset me most in the first half was the lack of enthusiasm. Where does that come from? The team energy, the attitude to receive the ball, the body language, the communication and the interplay that we just didn't have.’
Bristol Rovers 2-1 Shrewsbury, Charlton 0-3 Blackpool, Fleetwood 1-1 Accrington, Ipswich 2-1 Doncaster, MK Dons 1-1 Oxford, Rochdale 0-2 Burton, Swindon 2-1 Northampton.