Heya! The AO3 team is probably going to have to work out their encoding issues, the CSV is outputting UTF-8 characters as Windows-1252.

For now, you can fix your garbled tags using this online encoder: http://toolswebtop.com/text/process/encode/windows-1252

Leave source encoding as "auto" and paste in your text. The file uploader may take a CSV, I'm not sure. When I pasted in your examples I got these back, which are correct tags.
レ・ミゼラブル 少女コゼット | Les Misérables: Shoujo Cosette
文豪ストレイドッグス | Bungou Stray Dogs

Hope this helps?!