Wigan Athletic boss refuses to point the finger after Preston setback
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Latics led at the break thanks to Christ Tiehi, whose goalbound effort was helped into his own net by North End defender Greg Cunningham.
But two goals in the space of four minutes shortly after the restart turned the game on its head.
Hesitation from Latics goalkeeper Ben Amos saw him collide with Daniel Johnson, who picked himself up to convert the spot-kick.
Then Tom Cannon raced clean through to bury his first goal for the club - and consign Maloney to his first defeat as Latics boss.
Although the game-changing penalty decision appeared harsh, the Latics boss was in no mood to look for excuses after.
"I don't think we performed quite well enough to win it, but I also don't think we did enough to lose it either," he said.
"There were some big moments in the second half when we didn't defend well enough, and do the fundamentals you need to do well enough.
"That's why we lost two goals, which have cost us.
"The penalty decision was obviously a big moment, but how we got there was probably more disappointing.
"I didn't think it was a penalty, but the ball came from deep in the Preston half, and we just didn't do what we've been doing in the last four games.
"We have to match runners, the real basics of defending, and if we have to stop the game, we stop the game.
"I just don't think Preston had to work hard enough for their goals today.
"And that'd probably the most disappointing aspect of the afternoon.
"It's a big blow, it's our first blow, but these players have been fantastic for four games.
"But even winning at half-time, I wasn't happy with parts of our play in the first half.
"We could have been so much better, but it's all about how we respond now, and we have to go again Monday."
The opening quarter of the game was fast and frenetic, as expected on derby day with the stakes so high.
Latics were playing some good stuff, though, and they took the lead on 27 minutes.
Tiehi hunted the error as North End tried to play it out from the back, and exchanged a nice one-two with Ashley Fletcher.
From a tight angle, he fired towards the far post, with Cunningham applying the final touch as he tried to clear
The sound of North End being booed off at half-time would have been music to all of a Wigan persuasion.
But the game was turned on its head inside the space of four minutes shortly after the interval, with Johnson and Cannon putting Preston ahead.
Tom Pearce and Danel Sinani took over from Tendayi Darikwa and Will Keane, and the on-loan Norwich forward was quickly into the game.
After seeing a shot from 25 yards deflect just wide, he tried his luck again from even further out, only for Preston goalkeeper Freddie Woodman to pull off an incredible save with his right hand.
North End had substitute Robbie Brady red-carded in the dying seconds for a late challenge on Jack Whatmough.
But Latics couldn’t make the extra man count despite more than 10 minutes of stoppage-time.