The Millwall manager's later understanding contrasted sharply with his frustration in the immediate aftermath of the match. "I have just watched it on video and he blew the whistle before the ball went in the net," he said.
"We weren't sure whether he was going to give a penalty or whether he was going to give a free-kick for us. Andy Marshall stops and [Jorgensen] gets a toe to it and it goes in - bizarre.
"It has cost us points. I hope there was an assessor here to have a look at it because things like that cost you. I think the first foul was on Tony Craig. After that Tony did foul him but we deserved to win the game and it ends on that note, which is disappointing."
Coventry manager Micky Adams was equally perplexed by the incident. "When [the referee] pointed the other way I thought he had given a foul on one of the Millwall players, so nobody was more surprised than me when he gave the goal," he said.
The result prolonged Millwall's poor home run in front of their lowest crowd of the season. They have failed to win at The Den since Boxing Day, but that looked likely to change when Jody Morris converted a 69th-minute penalty after Trevor Benjamin handled.
Before the breakthrough, Millwall, who were without the injured Danny Dichio, struggled to find any rhythm. Morris toiled in midfield while Peter Sweeney offered a threat from the left, but Coventry goalkeeper Ian Bennett was rarely tested.
Bennett did come to Coventry's rescue in the closing stages with saves from David Livermore and Barry Hayles. The importance of those saves only became evident when Jorgensen brought parity with his contentious goal in the 89th minute.
Wise now admits that anything less than a victory at The Den against Plymouth on Sunday will signal the end of his team's promotion challenge. "We must win or I would say we are out of the play-offs," he said.
