Forest Green boss Ian Burchnall felt for Dion Charles after the forward was sent off in a “very unfortunate” mistake from the officials.
Elias Kachunga appeared to lash out at Brandon Cooper off the ball, but it was Charles who was shown a straight red card by referee Tom Nield after consulting with the linesman.
The Northern Ireland international had earlier opened the scoring with a clinical volley after getting on the end of Gethin Jones’ cross.
Despite playing more than an hour with 10 men, Ian Evatt’s men held on to secure a big three points as they aim to consolidate their place in the top six.
Burchnall said: “I didn’t see it at all. I saw absolutely nothing, but I spoke to Dion Charles as he came off and a couple of their staff as we came off at half time.
“They said it was a sending off but they got the wrong person. As I understand it, Kachunga was the one who raised his arm.
“The linesman has seen something but they have obviously made a mistake. If it is a red card, then it is a red card.
“But it is just very unfortunate for Dion Charles that he has been sent off because he didn’t deserve to be.”
He said: “I think any time there is a sending off, it kind of galvanises the team to be a bit more resolute defensively.
“I thought they were quite open in the first part of the game. But they did what they needed to do to get through the game, and credit to them for that.”
Forest Green had plenty of the ball in the second half but failed to test James Trafford in the Bolton goal.
Their best chance fell to substitute Mathew Stevens, who bundled wide from close range after the hosts were undone by Jordon Garrick’s flick on.
“It is frustrating to watch that,” said Burchnall. “Maybe if it is 0-0 it is different because Bolton maybe open up a little bit more. But at 1-0 they sat deep and I cannot blame them one minute for that.
“They defended the box magnificently but I really don’t think we challenged them enough. We have got to commit into the box far more than we did tonight.
“The delivery into the box was rushed, it was poor quality and we didn’t give the strikers on the pitch enough opportunities.
“The midfield have got tot get into the box. We have got to throw everything at that situation and sometimes I didn’t feel like we did. We held back a little bit.”