Wilks was withdrawn just after the hour mark as Rovers beat Luton Town on Saturday and trudged off the field, shaking his head.
McCann grabbed the on loan Leeds United forward and had a word in his ear, explaining afterwards that he did not appreciate the negative reaction.
'He is frustrated, he's a 19-year-old kid,' McCann said.
'I don't like bad reactions. I think I could see a little bit of it in his demeanour as he came off.
'I think it sends a signal to the rest of the stadium.
'But he's young, he's learning.
'I'm sure he'll get taken off plenty more times in his career.'
McCann explained he had taken the decision to withdraw Wilks due to noticing fatigue in the striker.
But he also noted Wilks still has plenty to learn about the style of play the Rovers boss favours.
'It's something young Mallik has to learn and we will teach him, he let the Luton full back out too easily,' McCann said.
'And when we switched him to the other side he let the other full back a bit too much.
'James Coppinger didn't because he picked up clever positions.
'Mallik is going to learn and I think he was much more of a threat when he went up in a two with John Marquis.'