Hola Wylie

This is a tricky one. When we want to say that "you don't think something has happened" in Spanish, the more direct translation would be that using the present perfect subjunctive "...que hayamos hecho..." and to go further back in time, as in "that we had done" we would still use the same "...que hayamos hecho" although you can also use "...que hubiéramos hecho..." If we decide to use the pluperfect subjunctive with hubiéramos, I think we'd want to convey, more than the "anteriority", the "uncertainty", as if we were saying "I don't think we had done something wrong (at least we don't think so, maybe you do...).

Also, using the pluperfect subjunctive could also change the meaning of the sentence and we would be meaning "that something would have/haven't happened". See this example:

This is not refering to something that "had happened" but that "would/not have happened". 

So, as a conclusion to your question, I'd say that you can use it with the pluperfect subjunctive but it doesn't really add any difference to the use of the present perfect subjunctive when you refer to a perfect action in the past; in fact, it'd be more commonly used with the pluperfect when we want to convey something that "would have happened". 

I hope this is clear enough to clarify your doubt. A tricky one as I said. 

Saludos

Inma