H1B petetion I797B expirary date mismatch with employment date on I-129

In got my fresh H1B petetion, wherin I-797B has validity date as 01/10/2012 to 30/09/2013 and in I-129 employment date is 01/10/2012 to 09/30/2015. Is it any issue? Can I fill DS160 and apply for PA date with Mumbai consolate?

It is not an issue. Your employer requested for 3 years, but USCIS approved it for 1 year. You should complete DS-160 form using 797 dates and not I-129 dates.