Stubbs is upset with his former managerâ€™s initial offer of ÂŁ28million to sign Leighton Baines and Marouane Fellaini, a valuation described as â€śderisoryâ€ť by Everton.
"I had no problem with David leaving for Manchester United. As managers, you have to be ruthless and make decisions that are not going to make people happy," Stubbs told the Daily Mail.
"I think Everton fans wished him all the best. Now heâ€™s come back for two of our players, he is public enemy number one. Thatâ€™s football. Heâ€™ll have to accept that.
"Heâ€™s said in the past Everton donâ€™t sell cheap and then comes in with a ÂŁ28million bid for I think the best left-back in the country and one of the best midfielders.
"We all play a game, managers and clubs, when it comes to signing players and obviously it was a first offer. But it wasnâ€™t the right first offer.
"There is a way of going about things. You have to be careful how you negotiate and donâ€™t pee people off. Being realistic at what other players cost, you can start talking ÂŁ35million and move from there.
"But it might take a bit of pressure off Wayne Rooney when he comes back to Goodison because he wonâ€™t be public enemy number one anymore. So heâ€™ll be happy!"
For the big stories and the banter follow us on Twitter: @tribalfootball