Sangram, SEBC is a State level registration because it is not available in all States. And NTA released a National level application form. So you will not find SEBC as a Category in the NTA Application form. And so you have to choose between General Category and OBC. Now if the Community you belong to is listed in the Central OBC list  then you can select OBC or else you have to select General Category and hence you chose General Category based on our previous discussion. But when you fill the State Application form for Counselling, yu will select SEBC as it is your State Counselling and you belong to SEBC. This is how the process works and your application will not be rejected for this reason.