Your percentile is not the only deciding factor for IIM Kozhikode admissions. I have seen instances where people with 99.78 percentile couldn’t make it while people with lower percentile and CGPA made it into IIM Kozhikode.
This is because IIM Kozhikode prefers a balanced score in each section and a good overall score. It even considers your 10 and 12 marks. They also pick students from versatile backgrounds.
Low CGPA is not an issue for admission into IIM Kozhikode. Your overall score should be appealing enough to get you in.