Yes, filling OBC in your MHT-CET application when you are not OBC-NCL (Non-Creamy Layer)  might affect your eligibility and potentially your percentile calculation  in a few ways:

MHT-CET reserves seats for various categories, including OBC-NCL. If you are not OBC-NCL but applied under that category, it's a discrepancy in your application.

During verification, the authorities might disqualify your application if you don't possess the required OBC-NCL certificate. This could affect your eligibility for any OBC seat allotment.

If you are disqualified from the OBC category, you'll be placed in the general category for merit-based ranking. This could potentially affect your percentile since the general category might have a higher competition level.

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I hope it helps!