Both goals came in the second half, Jermaine Beckford putting Bolton ahead before Alex Baptiste’s own goal saw Wednesday equalise.
Two controversial decisions then came with Johnson’s disallowed goal for offside and then Semedo’s reckless challenge seeing them down to 10 men with five minutes left.
Jones was not happy and stated he would appeal Semedo’s red card.
“It wasn’t a sending-off,” he said. “They had a youngster who should have been sent off and it should have been a goal.
“Hopefully, Chris (Foy) will review it and see that the lineslady was very quick in lifting her flag and I can’t see where the offside is.
“As for the red card, you can normally tell by the reaction of players and that’s what Semmy is all about and that’s not his game.
“That’s why he was so upset. His foot has slid across the floor and he’s taken the ball. I just feel that some of the big decisions weren’t right and we’ll certainly be appealing.”
Jones was pleased with his side’s performance, though, and added: “I can’t fault my players’ efforts at all because they were fantastic throughout and we’re doing everything right.
“Chris Kirkland has pulled off two terrific saves at the end but up until the sending-off there was only one winner for me.”