Can wrong category mentioned in 12th registration form be corrected

Though you have indicated yourself as being a general candidate in your registration form of your class twelve board by mistake but it could be taken otherwise from the different authorities. Even this amounts to suppression of facts from your end and sooner you take the corrective steps, the better.
You will have to write to the Board Secretary regarding your gross mistake and send the application along with the supporting documents for getting it corrected from the office of the Board. You will have to preserve the acknowledgment receipt which the receiver gets after getting the registered letter from the addressee. This receipt would be indicative of your honest approach to take proper initiative to rectify the mistake committed earlier.
Once this is acceptable to Board Authority, your battle is over.
After the correction, you would not face any problem in your JEE main counselling.

If the selection is on the basis of Category, there are possibilities of confusion. Otherwise there will not be any problem but however on selection, it is good to you to inform the concerned authorities to correct the records at that time. This would helpful to you in future for any allocation based on the category.

Actually, the information given in the application form should be correct. Any false information provided may be viewed seriously and sometimes there may be some punishments also.
When did you take your Caste certificate? Is it dated before your date of application for registration? It can be considered a mistake if it is dated before your application for registration. By mentioning the caste as general instead of OBC, the candidate is not claiming any additional concessions. So there will not be any problem.
You might have sent your application through the school you are studying. So meet the HM or the Administrative Head and inform them about the mistake you made. Give it in writing so that they can inform the board accordingly. When you submit your letter informing the mistake take an acknowledgement for your records.
In your all application in future please mention OBC only. Never mention as General. Always attach a copy of your caste certificate.