Sometimes production houses tend to adapt the story line a bit or go in a completely other direction. Why? I don't know exactly, there could be multiple reasons.
but fr instance Hellsing made it's TV adaptation, which wasn't all that bad. However the readers of the manga found a lot of differences, and were not happy about the animated version. Later a new version labeled as an OVA (Official Video Animation) was produced, which had it's story based and continued like it went in the manga.
A pretty much similar thing happened with Full Metal Alchemist, where the story very deviated from the original manga concept( which was later reproduced as Full Metal Alchemist: Brotherhood).
Reason mostly vary but it's mostly because production houses do stuff on their own and then mutate the storyline.
During the development of the anime, Arakawa allowed the anime staff to work independently from her, and requested having a different ending from the one in the manga. She said that she would not like to repeat the same ending in both media, as well as to make the manga longer to work more in the development of the characters. When watching the ending of the anime, she was amazed about how different the Homunculi creatures were from the manga and enjoyed how the staff speculated about the origins of the villains.
For instance... (source)