In a fictional text, ellipsis is most commonly used to indicate a long pause or hesitation in dialogue, reflecting a character's uncertainty or contemplation. It can also suggest an omission of text or a trailing off of thought. However, while it can indicate confusion, that is less common compared to its primary uses of showing pauses or omissions.
So, to summarize: ellipsis is primarily used to indicate a long pause or to denote an omission.