Just saving this post for the reference for future aspirants. One can read the comments made by the IITR professor justifying 0.33. Had I given GATE and suffered this I would have gone to court against this stupidity.
It is quite unfortunate. Never before have such a mistake happened in GATE. Human mistakes like wrong question/options have happened but at those times they have tried to correct them as much as possible. IITR just brought IITs to a normal engineering college level. It became an IIT only in 2001 and probably those not qualified to be in an IIT are still there. Hopefully, you can get to IITK and no need to worry about BARC because IITG/H is any day better.
Yes, If you see the spreadsheet entries 103 and 104 you can know that this issue happened this year - many other entries too but this is one where even score changed. And this is accepted by IITR though just tried to justify it showing "0.33" in the question page. For the 1/3 on the information page and on the brochure they have no answer. I'm not blaming IITR alone because I had mailed this to all IITs and no one care for this. And how I was sure of this issue- because I did the mark estimation on that google sheet from normalized marks and it was not matching. Then I also had the data from the answer sheets being submitted for rank evaluation and checking that revealed the reason of negatives.
How I'm sure this never happened before? Till whichever year GATE provided actual marks, it was always ending in 0.33, 0.67 or 1. IISc for example have published this in their site as cutoffs and similarly many others. Even last year we had collected this data in spreadsheet and noticed no such anomaly.
Nothing is going to change now, but I hope there are no sufferers. Personally I would like to ensure all IITs fill their seats now - as that issue can affect even more students. I'm sure this issue won't happen next year, as even if they don't acknowledge the mistake I'm sure they know Mathematics.