此题正确答案是C.
① which / that had been made in Jane's test 是一个定语从句.
关系代词指物,既可以用which,也可以用that；由于作主语,关系代词不能省.
完整的句子是The teacher pointed out the mistakes which / that he thought had been made in Jane's test.
② he thought 是插入语,一个独立成分.
不要独立成分的句子更是一目了然：
The teacher pointed out the mistakes which / that had been made in Jane's test.
全句中文：老师指出了他认为是Jane的试卷中犯的错误.