Bruce labelled cash-fuelled City's pursuit of midfielder Wilson Palacios - who has since joined Tottenham Hotspur - as 'absolutely disgusting'.
The Latics boss furiously claimed that City unsettled Palacios, insisting that their approach prevented Wigan from tying down the Honduran on a new contract.
Whelan, though, told the Manchester Evening News: "I must say, City were extremely straight with us at Wigan when they showed an interest in Wilson Palacios.
Shocked"I was a bit surprised when our manager Steve Bruce had a go at them - I told him so.
"Wilson may have been a bit overawed when he played against City for us.
"It wasn't one of his better games and (City manager) Mark Hughes probably saw this and thought twice about taking him to City. I don't know, it's just my view."
Whelan added: "I feel sorry for City to an extent because, in my view, they have been subjected unfairly to some diabolical publicity while the transfer window has been open.
"City are a fine club but things have been souped-up and over-hyped and they've been extremely unlucky."