这个主要因为语序的问题:
We _____ found____out that he___had been ______ a thief for a longtime by that time .
A.had found,had been B.had found,was
C.had been D.found,was
译文:我们发现他到那时已经做了一段时间的小偷了.
(到那时是修饰从句的,而不是到那时发现这个动作)
参考:by that time 到那时;节止那个时候 一般与完成时连用.
We had learned 5000 words by that time when we graduated.