Bowyer’s comments arrived after Blues’ draw with Peterborough on Tuesday night, with former captain Dean - whose last first-team appearance was on November 23 - joining the Owls the following day.
Dean, hoping to earn a longer-term deal at Wednesday - or put himself in the shop window for a move elsewhere with his days at Birmingham being effectively numbered - said: “To be honest, I read that after their draw with Peterborough. It disappointed me if I am honest.
“He had never said that to me personally and to then say it in the press, I was a little bit disappointed with - especially as I was club captain and I pride myself on leading by example, day in day out.
I think he maybe just meant it in a different way in that the club had been in that situation for four years running and I had been a main part of that squad.
“I could look at it the other way and if other players such as Lukas Jutkiewicz (and myself), perhaps if we weren’t there, then perhaps they’d never have stayed up.
“He is just trying to change the culture and the dynamic of that dressing room with younger players which is what a lot of clubs are doing. I have no issue between me and the manager at all.
“It was a business decision (to move) and they were open with that and I accepted it.
"I never got comfortable, I said that in the starting interview here.