For example, a direct translation from Spanish to English would result in that:

* "Cómo funciona" -> "How it works", as in "tell me how it works".

* "¿Cómo funciona?" -> "How does it work?".

The auxiliary "do/does" really looks like an extra unnecessary word, but omitting it sounds wrong to a native speaker or anyone already more used to English.

Part of the confusion could be because sentences like "but she does write" and "but she writes" mean basically the same thing (they imply different emphasis, but you know what I mean). So if someone incorrectly does pattern-matching based on those examples, I can see them thinking that "how does it work?" and "how it works?" mean the same thing.

After all, the "-s" suffix kinda looks like an abbreviation of "does", the same way the "-'re" suffix is an abbreviation of "are" ("writes" vs "does write", "they're" vs "they are").