Going a goal down inside the first minute after being caught off guard, they left themselves with a mountain to climb.
And their luck was out when, at 2-0 and a chance to get back into the match at the beginning of the second period, Amari Miller had a penalty saved by Sam Tickle.
Wigan knocked Blues out of the FA Youth Cup in the Fifth Round and are now 15 points clear at the summit.
Blues again fielded a predominantly young side against the Latcis, whose scorers were Sean McGurk (two) and Tom Costello.
Blues: Clayton, Sullivan, Powell, Noakes, Fogarty, Craig, Campbell, Walker (Bellingham 89), Zohore, Williams (Chang 64), Miller. Subs not used: Rouse, Djurovic, Scanlon.