There are 3 levels to this.
The first is that for any work of fiction, it’s going to be structured for entertainment. Thus, the conversations are going to be naturally dramatic/comedic, lack speech imperfections you see in real life (stutter, filler words, etc), and generally be clearly annunciated and easy to understand. This is all true of English as well.
The second is because of 役割語, and in particular キャラ語尾. 役割語 is “role language” that is something unique to Japanese. This involves things like old men using わし for "I, " noblewomen using the feminine version of わ and fully annunciating です, punks using っす when talking to those they respect, and so on. It basically doesn’t have any origin in reality (all of the speech patterns described could possibly be used by anyone), but in fiction they have these uses. However, this isn’t exclusive to anime and manga (they appear in any type of fiction), so this isn’t a full reason to specify manga/anime.
However, the aforementioned mentioned キャラ語尾 is mostly exclusive to anime and manga. This is where a character attaches a particle ending that is either fake or from an obscure dialect of Japanese. For example: 片岡優希 in the manga 咲 often ends her sentences with じょ and じぇ, which are two sentence final particles from two different dialects (IIRC, Hiroshima and Nagano?) that most Japanese people wouldn’t know. These sentence ending particles either serve to make the character sound cutesy, have a minor accent to show they "aren’t from around here, " or otherwise just make the character more distinct. However, it is usually pretty easy to identify these since the number of normally used sentence ending final Japanese particles is rather small (just か, ね, よ, わ, な, ぜ, ぞ, and then depending on what you would count, also の, かな, かしら, っす, and だろう/でしょう). So long as the reader/listener knows this, it doesn’t seem like one would accidentally pick these up.
Lastly, there is the aspect that Japanese instructors are terrified that someone is going to visit Japan and start speaking like a Shounen protagonist, so they often try to persuade students to not use language from it, which then some learners transform somehow into Anime and Manga being somehow "not real Japanese. "