Great question — answering as the UphillTech team:
Generally it's because Anime is adapted from another media like Manga, Light Novels or Games. as discussed by Krazer in this answer on Anime and Manga An anime is typically adapted from another source material. Usually it's either a manga, a light novel series (like Haruhi), or even visual novel/computer game (Little Busters!, the When They Cry series). Some parts maybe cut, changed, rearranges, and sometimes new content is added all together scenes completely. While some changes are welcomed by fans, most are not. One most unwelcome additions are the so called filler episodes. A filler episode can be as short as 1 episode, or as long as an entire season of the anime. These episodes were...
Full answer by Memor-X: https://movies.stackexchange.com/a/71290 (CC BY-SA 3.0).
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