I've learned a little bit of two other languages (Spanish and Japanese) and I'm pretty confident that most languages have a ton of nuance like this that you will never understand until you are actually totally immersed in that language and culture.

I mean, everything I learned in Spanish and Japanese is all super formal. Nobody actually talks that way IRL. There's words that from a translator or dictionary mean one thing, but are colloquially used totally differently. Like calling testicles eggs or nuts. "Chupa mi heuvos." They're not saying to suck their literal eggs.

I know less Japanese than Spanish but I already notice that, like, "no" isn't ever annunciated the way I'm being taught. Instead of "iie" I'll often hear just "ya." It teaches to end every statement with "desu," but I have never heard a sentence end with a desu or desu ka in any Japanese media (which is more than just anime). It's all way more casual. Questions are still understood to be questions if you use the right inflection; no need for extra syllables.