I read in a grammar book that -ja- can be roughly translated as "not yet", but when I tried "You haven't yet eaten oranges", it was rejected. Am I wrong here, or should this be reported?
It's better to think of -ja- as "haven't". The word "bado" is used to provide the emphasis that "yet" does in your sentence, so I think it was right to reject it.
No, "not yet" is completely right - the -ja- tense ALWAYS :) implies that the possibility (or even intention) for it to still happen exists. Therefore it should definitely not be marked wrong. Report it (I am.).