Such technical errors are better avoided but in your case, I would be surprised if they disqualify you. Disqualification is given if there is falsification of data, date of birth, income, reservation eligibility or fake degrees etc.
Yours is more of a technical issue. Good thing is that you have given an affidavit, and you have finished your medical. You have a graduation marksheet and online application that DOES NOT have your mother's surname. You have your 10th and 12th marksheet that has your mother's surname.
Please decide what her name should be, because you need to get this sorted for further issues like visa, health benefits etc.
What you have entered in the online application should match what is in your certificates. (https://railwayrecruitmentgov.in/document-verification-railway-2018/)
If you have time, take the affidavit and meet the 10th and 12th school authorities and get your mother's name changed to what you have entered in the application form. This can be done by the school prinicpal/ state board or the CBSE board.
You would need the affidavit, correct name published in two newspapers ( one English and one regional language) and the required fees for the service.
I would suggest, if you do this change then all the other documents would be in line by the time you are called for the final process of joining the job. If you have the address of the recruitment officer, you can send the changed doucment's attested copies by registered/speed post(for instance for the RRB, Bhuvaneshwar, the address is Assistant Secretary, Railway Recruitment Board, Bhubaneswar – 751023,). If you are sending documents, please ensure that you write clearly your name, application number, exam roll number, post applied for and the date of DV.