How about the idea that there's another knytt/wadf causing trouble in a town or with npcs, with the idea being it's a throwback at the beginning, due to something like a time distortion or imposter, where you had to complete another task. Such as picking flowers or moving stuff around on the 1st quest, but later on you're tasked with fixing this problem because it keeps happening to the townspeople over and over again.
Haha, I like that too. I just need to know an explanation that's logical enough so the player will understand what happened and why.
While you're working on a quest to collect flowers, you run into it. (Assume that the other Knytt/Ball is an ice ball.) Once it sees you, it runs away. If you track it down and calm it, it tells you that the person you're doing the quest for force-fed him the flowers. Like the red flowers in Cave Story, it turns that Knytt evil. The guy then sent the Knytt/Ball back in time. Then the Knytt/Ball dissapears in a flash of bright light. If you confront the quest guy then, he remembers nothing.... If you give him the flowers before tracking down the Knytt/Ball, he'll feed you the flowers, but you'll die when he tries to send you back in time.