That woman, she hates me. She wanted to make sure I never mastered genjutsu.
Here's a version I think you will like better:
That woman, she hates me. She wanted to make sure I would never master genjutsu.
(This is similar to "She wants to make sure I will never master genjutsu," but with everything shifted to the past.)
The sentence you took from the audio might sound strange to you, as an English learner, because it is the past subjunctive. Here's another example:
I'd rather your boyfriend stopped calling you in the middle of the night.
See, for example: http://www.grammaring.com/past-subjunctive