Difference in surname spelling in documents

In all of your document like Aadhar card, PAN card, ration card, voter card, High school marksheet, or any other educational credential if your surname and parents surname is same then it means that it is consistent in your records. So wherever your records will be seen, you will not have any problem. but the places where your parents document is also asked and cross checked with your document then problem will come because there will be a mismatch. In my knowledge, I don't know any situation where your parents documents will also be asked. Generally the student's documents are taken as granted and that is sufficient for the purpose. So, until and unless you meet certain specific condition where your parents certificates are also asked then only this problem would come.
For example if you go for renewal of your PAN card or reissue of your PAN card because it is lost or something like that then you will have to mention your father's name and at that time there will be a mismatch and then they will ask you what is the exact name of your father and then at the time you will have to correct it there itself to get the PAN card issued otherwise they will not issue it.
I am not sure whether any such situation can arise when you go for document verification for some entrance exam or some job position, so right now there is nothing to worry in the matter. Let us also see what is the view of our other experienced members in ISC about this issue.

A parent's document is rarely asked for something. When it is demanded and match with your document then a problem may arise. Otherwise, you would never feel any problem. As you mentioned that your all document having the same surname and it is differently found only in parent's documents. So, there is no need to be worried about this. If such a situation come then you should consult a legal advisor. They may help you in this regard.

There should not be any problem if all your documents are having the same spelling of your Surname and your father's surname. Whether to get admission into a school or get into a job, generally, the documents that will be verified are only yours but not your parents. These days the birth certificate is also very important. Please check that also once and see how is the name of your father in that certificate.
But sometimes when the property issues come. some may require to verify your father's certificates also. For example in the 'will' written by your father if he writes his name as per his certificates, there may be an issue.
What I suggest you is to make an affidavit in which it can be mentioned clearly that the two spellings belong to the same person only. You can contact a lawyer in your area and explain the problem. He will guide you correctly and you can make a legally valid affidavit.

The correction in your case is necessary.
If you are belonging to the states other than Tamilnadu and Kerala, surname, village name or family name are most important as it very much important in the states other than Tamilnadu and Kerala.

You first of all approach any nearby aadhaar center or e_center organized by your state government. Explain patiently to them with a copy of aadhaar of your father or mother or both. They will arrange for correcting your surname in your aadhaar with a correct one.
Secondly as for as your school certificates concern, you approach the school education department with the copies of aadhaar of your father or mother or both, explain to them for getting correction in your certificates. You approach the authorities in person and you take your father with you and explain in detail to them.

The certificate issuing authorities cannot be blamed for spelling difference as many people do have their names with different spelling in the thought of numerology and practice of their own area. In Pondicherry area people write Mourougan for Murugan. In Kerala Mani is written as Moni. In Bengal area Vasu is written as Basu.

It is common to have some mistakes while entering name/s in certificates and it is our duty to check while receiving. This may be due to the steps of both sides. While furnishing our name in application we should take utmost care as a)with or without space b) when we follow some numerology adjustments.

Being Exact detail on all the document is the best one. Few can be avoided or ignored if slight mistake or letter is missing and few can be corrected in the beginning itself to avoid any consequences sooner or later.

In your case, you could have avoided it in the beginning itself. Anyhow, still you can do it now by approaching the concern authority of the respective documents issued. Ask them how to correct the surname on the document. They will guide you on this therein.

Also, if not, when someone asks about the letter changed or missing it then you can verbally explain on this right away and such question will be very rare for sure.

I personally think, most of them will accept the surname in your case for sure. One letter missing or extra in the name or surname doesn't make much differences in general pronounce unless there is huge impact or its meaning differs entirely. Like Patel or Patil. Both different surname and need to be careful on checking and update it for sure.

As far as my perception, if the documents under your possession such as Aadhar Card, PAN Card, your Certificates relating to class ten and twelve and accompanying marks sheet don't indicate any discrepancy, you are not likely to face any issue in case of your document verification.
Whenever you face any interview for any government job or otherwise, you will be asked for the production of your documents and they will how far they are devoid of discrepancies in relation to your name, surname, date of birth etc. The same thing would be applicable in case of details of your father.
As you have indicated that the documents under your possession is free from such mistakes, you should not be unruly disturbed.
The discrepancies noted by you in relation to your father's certificates is not likely to affect you since the documents of your father is not likely to be presented.