For the most part, I have found that most of the levels (while not so obvious) always allow the entire group of 16 Zoombinis to complete a puzzle.
However, the last level where they are required to travel across the grid in bubbles, the last two attempts I have been unsuccessful in getting the entire group across, try as I might.
Is this planned?
Note: The first time, I only had 15 Zoombinis when I came to the last puzzle, and I only lost 1. The second time I had 16, but I lost 5. This may have some influence over what's currently happening.