"Please put that in a folder."
Translation:Bonvolu meti tion en dosierujon.
Because you have movement: now the item is not in the folder, after the putting it is in it, so it has moved INTO the folder -- EN la dosierujoN.
That would make it easier to know what the correct Esperanto sentence would be, but English is not quite as strict with maintaining the distinction in/into, on/onto etc. as Esperanto is.
"Put it in a folder" sounds better to me than "Put it into a folder".
"Put it in a folder" is colloquial rather than grammatically accurate. Duolingo has an odd relationship with translation, trying to walk the thin line between meaning and correctness. I would agree that the official translation of this from English should be "into" rather than "in". Let the secondary translation continue to accept "in" as an answer.
I still get lost sometimes between tio(n) and tiu(n). Since, presumably, the speaker and hearer know which specific thing should be put into the folder, shouldn't (couldn't) it (also) be tiu? I'm not grasping what makes tiu unacceptable here.
tiu is not merely used when you know what is being spoken about, but more specifically when you are singling out one item out of a group of similar items. It's closer to "that one".
For example, if there is a book, a newspaper, and a magazine on the table, you could point to the book and say "Put that into the folder" but not "put that one into the folder"... that book? There is only one book.
But if there were three books, you could point to the one in the middle and say "put that one (= tiun) into the folder": you are singling out one book from a group of other books.