Cambridge United boss makes Wigan Athletic promotion admission after victory
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Latics were hoping to go seven points clear at the top with four matches to go, but had a collective off-day at the office.
Goals from Harvey Knibbs and Sam Smith gave Cambridge a deserved 2-0 lead at the interval.
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Hide AdDespite Tom Naylor pulling one back with 13 minutes to go, Latics couldn't quite bring it back - with Will Keane being denied in stoppage-time by a fantastic save by Dimitar Mitov.
And Bonner felt his side should have put the game to bed long before that point.
"If I'm being picky, we should have been even further ahead at half-time, we should have had three goals up," he said.
"We should also have gone 3-1 up before our goalkeeper had to make a great save at the end, and we could have done better with a few counter attacking opportunities.
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Hide Ad"We allowed ourselves to get too deep in the second half, but it's difficult not to in those circumstances, against the top teams.
"We knew we'd have to be really good to win the game, and we certainly were, so I'm really thrilled."
Bonner had tipped Latics to pick up the League One title in the lead-up to the game.
And he saw nothing on Saturday to change his opinion.
"I do think they will win it, yes," he said. "They're such a powerful team, with so much depth, and so much attacking talent, and so much experience.
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Hide Ad"It's such a big achievement for us to have broken their record.
"But I don't see it all unravelling, they still have enough in their squad to get over the line.
"They'll still have a game in hand over MK Dons after this weekend, and I wish them well.
"I think Leam's done a brilliant job, and the way they play, and the way they conduct themselves - and conducted themselves today - is very good.
"This club should not be in this league after what happened."