Yesterday during JEE 2010 test, there was a mismatch in subject sequence in question paper and in answer sheet. Some of the students have given their answers as per the subjects mentioned in the answer sheet rather than question serial numbers. What will be the fate of such students where it was not clarified by the invigilators during the test. Will IIT JEE check these answer sheet in a different manner.
I undesrstamd your query. Under such cases usually decisions are taken in favour of students. While its considered as a responsibility of Invigilators and students themselves to clarify any doubts.
As of now you can wait, if this was a big issue JEE will come up with a better solution