If you have qualified CTET under the OBC-NCL category but applied for the EMRS TGT post as a General category candidate, your candidature is generally not rejected only because the categories are different. What matters for EMRS recruitment is the category you selected at the time of filling the EMRS application form, since that is the category under which you will be considered for merit, cut-off and reservation benefits.
Your CTET certificate remains valid for all categories as long as you have scored above the qualifying marks. CTET does not restrict you from applying to any recruitment under a different category. Many candidates qualify CTET under one category but apply to different teaching recruitments under another category based on their preference or documents.
The only important point is that at the time of EMRS document verification, you must be able to provide valid proof for the category you selected in the EMRS form. If you applied as General, you will be treated as a General candidate during the entire recruitment process, and no OBC-NCL benefit will be given. Since your CTET marks are above the UR cut-off, there is usually no issue.
So, your candidature is unlikely to be rejected just because your CTET category and EMRS application category do not match. Make sure your documents for the category you selected in EMRS are clear and valid. All the best.