when you read a manga or watch an anime and the events in it almost completely differ from its anime/manga counterpart?

for example: i finished watching eureka 7 a while back and i very much enjoyed it but, then i took a look at the manga version some parts were completely new and some events were different and the even the ending was different. I still enjoyed the series alot but, what i want to know is why does this happen in alot of manga/anime?