Since Steve Bruce joined as Latics manager, a number of his backroom team have since followed in his footsteps, with Birmingham reporting Wigan to the Premier League for what they perceive to be illegal approaches.
But Whelan has rejected those claims and is confident the whole matter will be thrown out when Wigan's evidence is presented.
He told Sky Sports News: "I'm very disappointed at Birmingham that they are pursuing this.
"We advertised for staff, they applied for the job, we interviewed them, they gave their necessary notice in.
"We've not taken anyone from Birmingham who didn't want to leave. I'm just disappointed at Birmingham for saying we've been poached their staff.
"They have reported us to the Premier League. The Premier League have now written us to ask for explanations. We can give them full written explanations and the whole case, in my opinion, will be dropped.
"So why bring it up in the first place. It doesn't put Birmingham in a good light. We haven't done one thing wrong."