You might have too many players with the same squad status, such as Key Player, and First Team. With this status, players expect to get played every week, and if they don't they will become unhappy.
Some players don't get on with others. In my game, I've had to sell Steven Taylor, because he fell out with Carroll, and half of my squad don't like Allan McGregor and Nile Ranger.
There may be other problems, but these are the most likely. To solve the 'player status' problem, you can change their status from first team to rotation, but they might become even more unhappy, so you are better off selling them, or offering them new contracts, with a different status...
...and if a player doesn't like another player, you can please your team by selling or loaning out the player. You will get a message, like, ''Olic glad to see McGregor leave''.