Warnock invited Leeds United to hire Hughes so "he could destroy another team of mine".
"I'm not going to sugar-coat what went on at the start of the season with Mark's situation," Bowen told talkSPORT. "We were 10 games into the season and without a win. There are reasons for what has gone on at QPR and what we inherited.
"We finished the season getting rid of 21 senior players who weren't, with all due respect to them, up to the Premier League.
"Out of all of the players that left not one of them went on to gain a Premier League contract. These are players who Neil Warnock had brought in to the club.
"On the first day we were there we noticed there were 10 or 11 players training on their own or with the reserve team coach.
"These weren't players who had a significant number of games in the league and equally they weren't players who were earning buttons at the time.
"Everybody knows the club has been in a huge transitional period but it does stick in my throat a bit that Neil has lost another job and started throwing mud around."