The event with the apple in chapter 3 is perhaps the first real indication that something is amiss with either Jonas or with his community. Readers are aware that the substance of an apple doesn't change, so when Jonas is throwing the apple with Asher and notices the "change," it presents a red flag for readers:

But suddenly Jonas had noticed, following the path of the apple through the air with his eyes, that the piece of fruit had—well, this was the part that he couldn't adequately understand—the apple had changed. Just for an instant. It had changed in mid-air, he remembered. Then it was in his hand, and he looked at it carefully, but it was the same apple. Unchanged.

At this point in the story, it is unclear what exactly has happened to the apple, and it isn't until Jonas begins his training that the change is made more clear.

In chapter 12, he notices that Fiona's hair experiences this same change. Jonas can't decide what to make of it, but he decides to ask the Giver about it. To his surprise, the Giver provides a memory of a sled, and he asks Jonas to examine it closely. Jonas realizes that the sled has the same quality as the brief change he saw in the apple and in Fiona's hair. The Giver teaches Jonas that, long ago, objects had a quality called color. It is at this point that readers grasp that Sameness includes limiting the ability of citizens' sight; thus, citizens in Jonas's world only see in black and white.

In The Giver, what happened to the apple when Jonas threw it to Asher?

In chapter three, Jonas recalls a time when he was indirectly chastised over the announcements for taking an apple home from the recreation area, which is against the community's rules. When Jonas recalls the incident, he remembers playing catch that day with Asher, and they were throwing an apple back and forth. Suddenly, Jonas noticed a change in the apple while it was in mid-air. However, the apple changed back to normal when he caught it. As Jonas continued to play catch with the apple, it would continue to mysteriously change in mid-air. Jonas found the incident very strange and unsettling, which is why he decided to take the apple home from the recreation area without permission. At this point in the story, Jonas is unaware that he has the Capacity to See Beyond and was simply seeing the color red in the apple. Essentially, Jonas was witnessing the apple's natural color before Sameness while he was playing catch with Asher.