So I started typing, and a window popped up and I have no idea what it was about, so I quickly closed it, and now one of my section folders has a little document icon on the folder icon.
You can see it here: https://imgur.com/a/1tMQ2W2
I have no idea what I did, or how to undo it. Would appreciate any help anyone can offer.
It means that the folder has body text. – That you wrote in it.
Folders are documents too, except that they behave differently under certain circumstances.
It may or may not be a problem, depending on your binder structure, and how you plan to format the whole at compile.
Anyways, lets assume that it is either useless text or misplaced text. Click on the folder, and display the editor in normal view.
You’ll see the text. Do what you have to do with it. 
. . . . . . . .
It is completely unrelated to whatever was your popup window.
Ah. That makes sense. Thanks!