Did you limit the height of the ScrollContainer? Generally, if you don't set the height property (or maxHeight), the container is allowed to grow as large as possible to display all of its content. Some layouts have additional properties that can limit the size too, such as the requested row/column count in some layouts.
Sometimes, when container grows larger than the stage, it will trick your brain into thinking the content is bigger than the container, when the container continues to grow just as large as its content, but is clipped by the limits of where OpenFL can render. In some cases, a parent container that clips, but doesn't scroll, could also cause this sort of illusion too.