It might be more obvious why it does what it does, if you see an example where the answers are more distinct.
All the mastery information is stored on the individual Japanese terms. When you do a quiz it is testing you on some of those terms.
Suppose you had a schedule with the a term that means woman: じょせい
And every time you had a quiz that asked you for the hiragana for woman you picked: おんな (which also means woman), and it always accepted that (even if the term it was trying to test you on was じょせい) (keep in mind one can also answer these questions by filling in the blank)
The result would be, you would never really be tested on whether you knew that: woman -> じょせい.
So, instead it gives you a message that basically means, "おんな is correct, so I won't penalize you, but I'm actually trying to test you on a different term."
So, the reason for the message is, it's trying to make sure you learn all the stuff in your schedule.
Similarly:
エレベーター, and エレベータ are two different terms that mean elevator. And it's trying to make sure you are tested on the term エレベーター, rather than エレベータ.
