Fillers are a given in most long running anime. If the anime is based on a manga then who writes the plot for the fillers?
Who decides the plot story for a filler season, so that it, for example, doesn't conflict with the original story of the manga?
Specialized or experienced writers, and the original manga writers can all work the manga into a plot for an episode, but why pay them to write a new scene where nothing interesting happens.
Generally 'filler' is made by cheap writers. As mentioned in the comments, there are often conflict because the filler writers are paid less and so put less effort into background work. Unlike lead writers, filler writers wont always be provided with reference material for things to include or avoid.
Basically, if it is irrelevant to the season's story line, has no effect on character development, you have someone who works for less write it. Although, filler scenes with no dialogue and no interaction, like someone taking an uneventful walk down a straight road requires no script at all.
As for who decides, whoever decides on the main plot will probably view the filler storyboard before it gets scripted.
Also, according to the TV Tropes page on fillers:
They are extremely common in Anime, where many shows have 26 or more episodes per season. The producers have to use filler just to meet contractual demands. Filler is usually something entirely original for the anime, but not always; many manga – particularly weekly manga – employ filler just as ruthlessly due to the extreme deadlines. Sometimes entire filler Arcs are created, most often because the series Overtook the Manga.
It's difficult to find information about who writes the filler arcs, but movies, which are similar in principle to filler arcs in that they don't interact with the main story line, are generally written by the same writer as the show. Bleach's movies, for example, are written by Masashi Sogo, same as the show. Because there are anime writers who are separate from the manga writers, they can add to the story without interfering with the work of the manga writer.
The fact that fillers are sometimes used to meet contractual demands makes it more likely that fillers will virtually always be written by the writer of the canonical anime, at least in those cases.
