Yes, manga can have fillers. Sometimes authors use them to flesh out characters or settings, or to give themselves more time to plan the main plot. But too many fillers can make the story drag.
It's fairly common. Fans often look for more content related to their favorite shows. Since 'Attack on Titan' has a large and passionate fan base, there are a lot of fanfics available. 'Aot' fans might watch (read) these fanfics to explore different scenarios that the official story didn't cover. For example, they might want to see how a certain character would react in a different situation or what would happen if a major plot event had a different outcome.
The Naruto manga itself doesn't have fillers. Fillers are a common thing in anime to extend the runtime or bridge gaps in the manga's story. But the manga sticks strictly to the main plot.