It just means that Netflix is the first-run exclusive broadcaster of the content in the regions where Netflix describes it as a "Netflix original". In its List of original programs distributed by Netflix Wikipedia lists Little Witch Academia in the "Acquisition" section as an "Exclusive international television distribution". It gives the following description of these types of shows:
These television shows, even though Netflix lists them as Netflix originals, are shows that have been aired in different countries, and Netflix has bought exclusive distribution rights to stream them in other various countries. They may be available on Netflix in their home territory and other markets where Netflix does not have the first run license, without the Netflix Original label, some time after their first-run airing on their original broadcaster.
So in the US, for example, Little Witch Academia is a Netflix original, while in Japan it would just be another old TV show in its catalogue. It can happen the other way too, where a show originally broadcast in the US by different broadcaster becomes a Netflix original when shown by Netflix outside of the US.