Why is Charlie having difficulty putting his feelings into words?
It depends what part of the novel you are speaking about. I'm guessing that you are referring to the beginning of the novel, before Charlie has his operation. In this state, he is required to begin a journal as directed by the psychologist who is running the program. Charlie has trouble putting his feelings into words because of his extremely low IQ. He has trouble even understanding his own simple emotions, let alone putting them into words.
At the end of the novel, Charlie has trouble because his IQ had begun to deteriorate. Not only is he returning to his previous IQ, he is getting even worse as he regresses to the point of death.