As per "Accounting Standard (AS-15) Employees Benefits" issued by the ICAI, every employer/assessee has to make a provision (mandatory) in their Annual Accounts towards gratuity for their employees using the "Actuarial" valuation method for those who have become eligible for gratuity under the Gratuity Act or any other applicable scheme. This provision is claimed as a deduction for expenses for the respective year for computing the employer's income tax. Failure to do so will result in disallowance in the future.
However, in your case, your firm has omitted one employee's provision for making a provision in the accounts, possibly due to oversight. You have not mentioned for which year this provision pertains to. Presumably, it should be for an incremental liability for the Financial year 2013-14, for which your firm might have recently filed the income tax return. I don't think this is a significant mistake to worry much about. If you are very concerned, discuss with your auditors. You might also consider filing a revised return since I am sure the assessment of the income tax return for 2013-14 is not yet completed. Even if the assessment is over, don't worry; ensure it is covered for the next year by making a fresh provision either under "Prior Period Expense" or under the Major Head Employees Benefits as the case may be.