in which table under table 6 or table 8. if you r talking about table 6 then it's not possible because you just need to provide bifurcation of tax which you claimed and if negative figure is coming in 8D then you need to find out reason of it may be supplier didn't file return and you had claimed ITC in this situation you just need to check if you have valid invoice then it's okay no problem file GSTR-9 with negative figure.