Britt Assombalonga put Posh on their way with a fine 25-yarder and then won a penalty which Lee Tomlin converted.
But Charlie MacDonald pulled one back for the Latics before James Tarkowski contrived to miss an open goal with the last kick of the game
Posh have reeled off four successive victories in all competitions despite not hitting top gear.
Ferguson said: "We have to count ourselves lucky to win that game.
"We had so many players who were miles below par and yet we still managed to come out on top.
"I'm delighted to be winning games as that is what this business is all about, but there is a lot of stuff that I am not happy with.
"We have not been anywhere near our best so far this season and we need to work out why that is the case."