Mismatch of name in graduation/equivalent certificate with that in matriculation certificate

It may not be a problem because the certificate given by the Air force contains your name as BEHERA SK. Anyhow to avoid any future complications you should have proof to show that SANJAYA KUMAR BEHERA and BEHERA SK are the two formats of the name of the same person only. There are two ways for it.
1. Apply to the Air force and get a certificate saying that your full name is SANJAYA KUMAR BEHERA and it is shown as BEHERA SK on the certificate given by them. You have to contact the concerned section and discuss with them and get the certificate.
2. The second way is to get an affidavit made in which it will be mentioned that BEHERA SK and SANJAYA KUMAR BEHERA are the names of the same person. One is the full form and the other is the shorter form. Once you have this affidavit with you, in case of any problem you can produce the same. For making this affidavit you have to contact a good lawyer, talk to him and get the same made.

It may not pose you any problem during the verification process if the verifying authorities are sensible and understanding the minor mistake that cropped up during the issuance of the certificate from the Air Force authorities. The mistake originated in the diploma reflected even in your graduation course.
It is not necessary that all the officials connected with the verification would be favourable always and hence remedial steps are necessary.
There are two ways of getting it corrected. Either get it corrected from the source from where it has originated ie the Air Force or approach a good lawyer for the process of affidavit to be released by the First Class Magistrate after getting the same countersigned by him.
The affidavit must reflect that both the names Sanjaya Kumar Behera and Behera SK represent the same person. Get it published in the English Newspaper apart from the Local Newspaper for wide publicity.
Retain its cutting to be used during the stage of verification whenever required.

It would not create any problems during document verification. As mentioned above in your Air force certificate your name is BEHERA SK. So, to avoid future problems you must contain two formats SANJAYA KUMAR BEHERA and BEHERA SK so that any documented problem may avoid easily.
There are two ways of getting it corrected. First, you get it corrected from the Air force department from where it has originated. And second, you should contact a good lawyer for the process of the affidavit. The affidavit should be made so that both the names Sanjaya Kumar Behera and Behera SK are shown on the certificate for the same person. Get it published in the English Newspaper. You should publish in the local Newspaper also for more publicity. Keep this cutting for future verification when it is demanded.

Thank you all for your valuable comments.

Any change of the candidate's name in his certificates or mark sheets is a matter of concern because the people who are doing document verification are always very particular about it and if there is any difference they will start asking questions as well as keeping the whole thing in pending until the necessary documents are shown to them.
It it is always a difficult proposition to get the certificates, mark sheets, and other credentials corrected from the origin from where they were issued as it takes time and generally it goes through some procedure so it is advisable to go for a legal affidavit where all these details are mentioned along with the copies of the documents and same is signed by the candidate and also countersigned by a court magistrate or notary public. This affidavit can be made with the help of a lawyer or by directly going to the designated notary public in the area.
Whenever there is a document verification then keep this original with you and give a copy of the same to the verifying authorities if they ask for it.