Jordan Storey put the Owls in front on 66 minutes following a goalmouth scramble after Barry Bannan’s corner kick was headed against the post by Harlee Dean.
Evatt said: “It was offside. They (the officials) have got to know the rules.
“If the keeper is out of his goal and there is only one covering defender, he (Storey) is offside.
“These big decisions in these big games you can’t get wrong. The linesman said there were two players behind the keeper; there was – one of theirs and one of ours.”
Evatt cut a frustrated figure on the touchline as several decisions went against his side throughout the match, which saw referee Carl Brook produce six yellow cards.
“I just felt like we were on the rough end of a few today,” he added.
Bolton equalised in the ninetieth minute through defender MJ Williams, who scored his first goal for the club to rescue a point.
“Considering the injuries and illnesses, we have done remarkably well to get something out of the game,” Evatt said.
“Arguably, we had the biggest chance in the first half through Jon Dadi Bodvarsson. He had to score.
“In the second half, they threw everything at us. But the goal is offside which is annoying and frustrating.
“We are competitive and we have come a long way. But it is now how we get ahead of these teams.”
Sheffield Wednesday remain fifth in League One following the result, which leaves them level on points with Sunderland and Wycombe below them.