Though many anime derive from manga, not every one of those anime follows its source manga closely. When it comes to anime that are different from the manga, plenty of examples come up. Differences between manga and anime versions can arise for all sorts of reasons: an anime geared towards kids may omit the violence seen in the manga or a studio may need to create filler episodes while awaiting the next manga chapter. You may not realize it, but Pokémon's anime and manga versions differ wildly.
Fans often bristle when their favorite manga aren't replicated faithfully. Imagine waiting for your favorite scene from the manga only to find it's substantially changed or entirely cut from the anime version. On the other hand, such differences mean each version can tell a vastly different story. Just look at the details left out of Akira from manga to anime. Occasionally, the original manga falls short of the anime, which can shift up the plot with exciting and unique filler sagas.
Though primarily based on a series of Nintendo video games, the Pokémon anime series did have a companion manga, and the two are strikingly different. While the anime follows the adventures of Ash Ketchum and Pikachu, the manga leaves Ash's equivalent, Red, behind fairly quickly, following the journeys of a wide variety of characters from different regions of the Pokémon world.
The manga also appeals to an older audience, featuring death, violence, and other potentially upsetting content. In this version, gym leaders and even members of the Elite Four partake in nefarious activities like those undertaken by Team Rocket.
When the first Hellsing manga was coming out, there wasn't a lot of manga material with which to work. This meant that the producers needed to come up with their own villain, a particularly powerful vampire named Incognito. Though the war-hungry Nazis of the manga briefly appear, they take a backseat to Incognito's attacks on the Hellsing organization.
Hellsing Ultimate, a set of OVAs which began airing five years after the initial series' 2001 release date, followed the then-completed manga more exactingly.
If you remove the filler, the Yu-Gi-Oh! anime differs very little all from the manga. Both tell the the same basic story of a boy possessed by the soul of an ancient Egyptian pharaoh. What truly differentiates the two is tone. While the Yu-Gi-Oh! anime certainly has dark moments, it's mostly targeted towards a younger audience. The manga, meanwhile, aims for teenage readers and includes graphic violence, much of which is perpetrated by Yami Yugi, one of the heroes of the series.
In the manga and Japanese anime adaptations, the Shadow Realm does not exist, and characters instead are subjected to graphic injury, torture, or death.
Because it frequently runs out of manga material to adapt, Naruto ends up bloated by endless filler arcs and episodes. Some of these excel, but others are quite lackluster, and all of them distract from the story. To avoid this fate, the creators try something new with Boruto, the series' spin-off sequel. The first 50 episodes of Boruto aren't based on manga material - they start when Naruto's son, Boruto, is still a young child in Ninja Academy, using the time to introduce substantial changes since the familiar series.
After episode 50, around where Boruto takes the chuunin exams, the series will presumably follow the manga more closely.