The big defender was penalised for handball 10 minutes into the game, not by referee Kevin Friend, but by linesman Anthony Tankard patrolling the touchline to the left of the massed ranks of Whites fans.
It was a head-scratching moment, with the referee having first indicated a corner before being crowded by half a dozen irate Latics players.
But while Mills protests his innocence in the piece, he admitted it was hard not to feel guilty after a good result was thrown away at the DW Stadium.
Describing the incident, he told The Bolton News: “The ball came over my head and I’m facing my own goal, I got a push in my back and the referee gave a corner.
“All of a sudden I see he has given a penalty because the linesman on the other side of the pitch has seen the ball intentionally hit my hand.
“I haven’t got eyes in the back of my head but how does he change his mind? I’m gutted for the fans, obviously.
“It’s the best atmosphere I’ve played under at this club and that’s what really gets me – let’s not beat around the bush, I cost us a goal.
“I don’t know how, but it is what it is.
“They supported us all the way through because they could see what we were trying to achieve.
“We were by far the better team.”
Wanderers quickly found themselves two goals down but fought back to 2-2 an hour into the game through Neil Danns’ header and Andre Moritz’s penalty.
Just a few minutes later, some poor marking at a corner allowed Callum McManaman to slam home a third for Wigan, leaving the Whites with another mountain to climb.
“We rallied at half time and I thought the comeback was fantastic but it’s disappointing we leave with nothing,” Mills said.
“If you are looking at any of the three goals, it’s the last one that you can be really disappointed with.
“We have been so good from set pieces – it’s been one of our strong points this season.
“It is difficult to say ‘slow it down’ because we had them on the ropes and the tempo was high. You can’t really say pack up and take a point.
“Looking back with hindsight you might say we should have kept a little bit back but at the end of the day it’s not as if they’ve counter attacked and played right the way through us.
“It was sloppy in terms of the organisation and the second phase.”