Leighton Clarkson had given the young Reds a one-goal lead prior to half-time before their League One opposition went on to stage a second-half comeback.
Goals from Kal Naismith, Joe Garner and braces from Charlie Jolley and Ollie Crankshaw ultimately secured the three points for the hosts.
Liverpool will look to respond in their next Northern Group D fixture when they travel to Tranmere Rovers next Tuesday.
Surviving an early scare as Wigan hit the post, Barry Lewtas' charges took control of the first-half proceedings.
Jack Bearne and Liam Millar went close to opening the scoring during the first period before the deserved opener finally arrived in the 44th minute.