Lately my Firefox has been showing a ligature for "fi" in monospace code blocks, showing those two characters in the width of a single character. On every website with code blocks. It is mildly infuriating and I don't understand it.

Right-click the ligature text -> Inpsect. In the Inspector, on the right there is a tab called "Fonts" (to the right of "Rules", "Layout", etc). That will show you what font(s) Firefox used to render all the text in the selected element.

I used Stylus to force ligatures off at some point, it mostly worked but caused some other issues.

Which is totally fine on their own machine, but using a webfont to force ligatures on anyone viewing their website is just confusing as a reader.

No, I get it. I don't use them either because I find them confusing. I'm just telling you you missed out on what was a quite popular trend from a few years ago.