Student or Learner
Is it referring to "past perfect" before "thought" or the same past tense as "thought"?
I learned conditionals don't change depending on tense change of the main clause, so it must refer to past perfect.
ex)I thought you would have finished your homework.
The person would start with the idea that the person will have finished their homework and then discovers that this is not the case, so it's just backshifting.