This depends a bunch on what part of the book you are talking about.
At the very start of the book, what is wrong with Jonas is that he is afraid. Or at least he is apprehensive. He is worried about what job he will be selected for when he becomes a Twelve.
Later on in the book, what's wrong with him is that he doesn't fit in so well anymore because he understands things his friends don't, like how horrible war is.
Finally, after he sees the video of his dad releasing the baby, what's wrong with them is that he thinks his society is evil and he wants to get away from it.
In the book The Giver, Jonas is different from the other children. He has lighter eyes and he must exhibit some features that lead the elders to believe that he will make a good receiver.
As Jonas begins to receive the memories he begins to experience things he had not before. He start to see color and he eventually experiences pain and suffering, death and destruction through war. Jonas begins to understand that he is becoming isolated from the others in the community. He now has thoughts that they can not understand or relate to.
After Jonas witnesses what release is and learns it is murder, he feels that he can not stay with the others in the community any longer. What is wrong with Jonas is that he has become a human being complete with emotions and feelings and worries.
Jonas begins to see a few things that change in his daily life, such as Fiona's hair and an apple. Jonas is confused and seeks The Giver. The Giver explains to him that he is beginning to see the colour, and Jonas is very fascinated by this new experience.
He was always born different, with lighter eyes and a tendency to be smarter than his peers.