Wigan Athletic boss rues 'two moments in the game' that cost his side at Burton Albion
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Latics had led 1-0 at the interval thanks to a Charlie Hughes volley moments before the half-time whistle, after Callum McManaman had sent another shot inches past the post.
But Joe Powell levelled with a superb strike from distance midway through the second period.
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Hide AdAnd Maloney's men slipped to a fifth defeat in their last six matches when Powell converted a late penalty, after Kell Watts was adjudged to have handled the ball from a Burton cross.
"I knew what kind of match it was going to be, it was never going to be an open, free-flowing game," assessed the Latics boss.
"Coming to a stadium like this, it was a real battle, but the performance was good today.
"Two moments in the game, two mistakes, cost us, but that's the level we're at.
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Hide Ad"I can't be too critical, because the players have given me a performance I wanted.
"At 1-0 up, I felt very comfortable.
"Maybe we didn't quite get what we deserved, a draw maybe..."
Latics slipped to second bottom in the League One table ahead of Saturday's trip to high-flying Stevenage Borough.
And having fought their way back from an eight-point deduction ahead of schedule, Maloney reiterated his belief that the mental barrier of the punishment is still affecting the club.
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Hide Ad"These results feel a little bit more because of the position in the table," he said.
"But it's okay, it's what we signed up for, and we'll go down this path.
"It's another sore one but we go again on Saturday."
Referee Sunny Singh Gill was surrounded by a number of Latics players after awarding the Brewers the match winning penalty.
Despite his side being denied a stonewall penalty against Portsmouth last Saturday, Maloney refused to use the incident as an excuse.
"I have no complaints about the penalty," he added.
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Hide Ad"I said at the weekend I thought the official got that one wrong.
"But I don't like criticising referees, and I had no issue with his decision."
Latics flew out of the traps and could have been ahead inside 30 seconds.
Skipper Josh Magennis raced through and saw his first shot blocked by a defender, before the rebound was deflected wide of the near post.
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Hide AdMcManaman - another of the six changes to the starting XI - came closer still when he fired agonisingly wide of the far post.
Burton sensed the let-off and came into the game, with Josh Gordon seeing one effort tipped over by Sam Tickle, and sending another flying over the top.
Latics took the lead a minute before the break, when Magennis’ long throw-in from the left was lashed home by Hughes on the volley.
James Balagizi appeared for the second half in place of Baba Adeeko who, on a booking, had committed a foul on the stroke of half-time that saw him given a lengthy lecture by referee Sunny Singh Gill.
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Hide AdBurton equalised midway through the second half when Sean Clare gave the ball away cheaply and Powell fired home from almost 30 yards
And Powell’s penalty secured the points, despite Burton finishing with 10 after Beryly Lubala was shown a second yellow in the dying seconds.