Roberto Martinez could not understand why Junior Hoilett's goal was allowed to stand during a 3-3 draw between Blackburn and Wigan.
Hoilett's 58th-minute effort came from a corner which appeared to be illegally taken by Morten Gamst Pedersen.
Striker Yakubu Aiyegbeni put the ball down on the corner spot, but appeared not to kick it into play.
Norwegian winger Pedersen then ran directly from the corner spot before setting up Hoilett for an equaliser, making it 2-2 with 30 minutes remaining.
Later, Wigan appeared to have won the match when Albert Crusat made it 3-2 with three minutes to go.
But Yakubu's penalty, struck nine minutes into injury time, salvaged a point for the hosts.
"I don't know what to say," Martinez said.
"If I'm going to be honest I'm going to get into trouble and it's going to cost me a lot of money."
"The decision is hard to take, hard to explain because I could watch it 10 times on the television and couldn't tell you what happened."
"On live it didn't seem he touched the ball, and for a referee to allow that is hurtful."
"As a referee I’m sure you have to watch the ball at all times."
"(The players) were confused, they felt Yakubu left the ball for Pedersen, after that they didn't know why it was allowed."
"It's my fault (they didn't complain), I force the players not to complain, not to get involved with dissent, not to dive and it's costing us points at the moment."
Blackburn Rovers manager Steve Kean claims to have been surprised by his players' unusual set-piece routine.
"I don't know if he (Yakubu) touched it or rolled it," Kean said.
"I’ve not seen it again but maybe he’s (referee Andre Mariner) thought he's got a full circumference on the ball."
"I was surprised when I saw him (Pedersen) running along the line so I just took it that he's just touched or rolled his studs over the top of the ball."
Kean also felt Mariner was justified in awarding the late penalty, given against David Jones for a high challenge on Blackburn goalkeeper Paul Robinson, who was in the opposition penalty area seeking an equaliser.
"I'm delighted," Kean said.
"We've had a lot of last-minute things go against us but I think the referee's justified giving the last-minute decision."