The Chesterfield boss was happy enough at half-time with the score at 0-0 and the Spireites seemingly well in the game.
But the second half brought three goals, one of them just three minutes after the restart.
And after that, Town failed to cope with a clinical, muscular Scunthorpe.
Wilson said the timing of the first goal was a huge blow for Chesterfield.
“To concede after three minutes of the second half was very disappointing,” he said.
“It was a soft goal as well, Jon Nolan gives a soft free-kick away. The free-kick that comes in is poor from our point of view. That put us on the back foot and I saw a Scunthorpe side full of confidence.”
“In the first half we stuck in, we were in it, but then we concede after three minutes of the second half and the other two goals were very poor. Two balls in behind us. Overall that’s possibly what we deserved.”
Wilson said his players didn’t battle hard enough to get back into the tie.
“We came up against men and we weren’t men today, we lost too many individual battles today,” he said.
“We need to provoke one or two performances for the next couple of weeks.
“I’m not going to make an excuse for it, we’ve got to make players out there who will put their bodies on the line and we didn’t do that today. They did. We can’t lose 50:50 battles all the time.
“It’s not just toughness in physicality, it’s a braveness between the ears as well.”
After just one win in 11 League One outings Chesterfield have slipped to second bottom of the table, four points adrift of safety.
Wilson says the only answer is to roll up their sleeves and knuckle down, but he admits their form isn’t good enough.
“We battle away, like we always have done. This is when we find out who are men and who will fall away,” he said.
“Who knows it could be me falls by the wayside with results like that. You don’t expect to be patted on the back for it.
“We’ve got to take the overall responsibility for it.
“They’ve got to perform next week, they’ve got to show this is a performance and a result that is unlike us today.
“We have to try and find a solution and we will do that.”