My marriage was on Dec 4 2006 in Kerala. But due to some issues, I have not applied for marriage certificate. Will it be a problem in the future?

The Common marriage Rules came into effect only on 29th February 2008. 

For marriages solemnized before 29th February 2008, registration is optional.

For marriages solemnized after 29th February 2008, registration is compulsory.

In case, you need to register the marriage, you have to get permission from the Deputy Director of Panchayats of the district where the marriage was solemnized and register the marriage first. For that, please approach the concerned Grama Panchayat/Urban local body.