Hughes knows that several players who have been told they have no future at the club are the source of his problems.
City have struggled in the League and have been knocked out of the domestic cups by lowly Brighton and Nottingham Forest.
A dressing-room insider told the Sunday Mirror: "Most of the players are right behind Hughes, but unless you have everyone pulling in the right direction at a club then you will get problems.
"That's what's happening here. Some players know they haven't got a future at the club and others just don't like the manager.
"Injuries and a lack of depth in the squad have forced Hughes to use players he doesn't want in his team - and that has been the root of his problems.
It's no secret that he is desperately trying to get new players in and trouble-makers out this month."