After the exit of an employee, the employer has deposited the PF contribution in his account after 2 years and now the employee is not able to transfer his PF to the new organization

An employee left the organisation in July 2007 and the employer erroneously paid his PF contribution after 2 years of his exit from the services, i.e. in the month of Sep 2009.
Today in 2019 when the employee wants to get his PF transferred to the new organisation, he is not able to do so as the PF office rejected the application form stating the the actual date of exit (as per the last PF contribution record with them) and the date of exit mentioned on the PF transfer form are different.
PF office is considering the date of exit as Sep 2009 as last contribution made by the organisation was that one.
How will this problem get sorted?

You have to sort out this issue with the employer first and if the employer had erroneously deposited the amount he should get it back. Only a joint representation can solve this problem.