1 I saw you ate
2 I saw you had eaten
3 I thought you were right
4 I thought you had been right
1 and 2 are clear to me. 1 at the same time 2 first eating then seeing for example crumbles. What about 3 and 4. 3 at the same time and 4 first being right and then thinking. It doesn't make sense to me. I think that I need to add something like "I thought you were/ had been right when I saw you". Why is that that when it comes to 1 and 2 I don't need to add anything but with 3 and 4 I have to.
The "past perfect" is used when the speaker is viewing events from a later (but still past) point in time. Sometimes that later point in time will be associated with a specific word ("saw" and "thought" in your examples) but sometimes it will not: it will already have been established in the discourse or (particularly in narrative) it may not have been mentioned but the use of the past perfect itself established a temporal viewpoint. (For example, a story might begin "He had been a moody child" - this establishes that the temporal viewpoint is later, when he was no longer a child, or no longer moody).
So your fourth example is fine as it is: the thinking takes place at a later time than the being right.
It's also worth noting that the use of this complex form is usually optional: English speakers often don't use it when the temporal relationships are obvious, or are unimportant. So your 1 and 2 could refer to precisely the same set of events, and similarly your 3 and 4.
