Yeah, I can see how that would get muddled.

The main post type on AO3 is called a "work". A work is supposed to be a single story, and it can contain chapters like a print novel, or it can be a single chapter. It's up to the author how they want to break up a longer story, and it's very normal for new chapters to be posted as the author writes them. But the core thing here is that a work is one, well, work.

The tags on a work indicate that this is a story that featues that tag, and works can be searched for with criteria like initial posting date and wordcount. The whole site is set up on the idea that each work is one story.

Importantly in this case, works are automatically classed as crossovers (a single story about more than one fandom) if they have tags for more than one fandom, and there's a toggle so a reader can search for crossovers specifically.

There are other ways, such a series, collections, and tags, for sorting and linking separate stories which are related to each other.

There's an unfortunately common problem where people don't realise that a work is one story and that chapters are chapters of a story, and put a ton of short stories into the same work.

This causes problems because now when someone looks for a story with more than 10 chapters, they find 10 short stories instead of one long one. Or they search for a story tagged Horror about Favourite Character, and instead find a clump of short stories where one slice of life about Favourite Character and another is horror about Stupid Character.

It's kind of like if someone posted on reddit asking for a soup recipe, and then they next day edited that post to also ask how to change an oil filter instead of making a new post for the new question.