The suffixes Kumar, Prasad, Das, Bhai, Mohd., Singh, Sinh, Dev, Kaur, Kumari, etc. are not as such considered while approving names in Official Gazette. Please note the School leaving certificate of 10th and 12th can be created duplicate by placing an application for change of father's name there on basis of other official documents of your wife where "Sunil Kumar Mondal" is written. Try out the same. If not possible then only go through the entire process as mentioned below. so far as passport is concerned you may place amendment of name application which can be done online through official website of Passport authority of India.
If none of the proposition as mentioned above works with you and still you want to do something to bring congruence in all the documents, then get an affidavit from her father stating that name " Sunil Mondal" and "Sunil Kumar Mondal" both belongs to him and wherever these names are used, the same belong to him. Get the same attested in Notary Public.
You can thereafter, annex this affidavit along with documents that you produce having two different names of Father of your wife and give one line clarification that as some of the documents disclose distinct name of Father, you have attached an affidavit to support common identity of her father with the form.
If her father isn't alive then she has to make an affidavit stating that the documents where "Sunil Mondal" is written and the documents where "Sunil Kumar Mondal" is written both belongs to her.