Jonas is starting to see in color. He is not taking the pills that the rest of his society is taking that create "sameness". So, Jonas is able to see everything for what it is. The first color he saw was red which is what happened to the apple.
As the book progresses, Jonas is given lessons in color, warmth, cold, and pain. Asher's assignment is to be Assistant Director of Recreation. Asher and Jonas fall out over the goodies/baddies game. Jonas knows the deeper meaning behind the game while to Asher, it is "just a game".
Jonas is discovering the utter aloneness that his assignment will bring to him, and as a result he discovers the horror of his perfect world.
When Jonas sees the apple "change" in The Giver, nothing is actually happening to the apple; the change is happening to Jonas. He is beginning to see color for the very first time. Since Jonas has no concept of what color actually is, he only sees it as a change in the object.
Once he is with the Giver, he is told that he was seeing the color "red" and he is told that it is one of the first ones that he (the Giver) had seen. As to why Jonas is actually seeing it, the answer (though never completely explained) is most likely in his pale, light colored eyes that he and the Giver share. These are unlike most of the other people in the community.