The word CTC means "Cost to Company." When appointing anyone in the organization, we assume that they will stay for a longer period. That's why we include the gratuity as part of the CTC. I believe you are not deducting it from their monthly gross salary.
Therefore, the company is liable to pay the gratuity only after the completion of continuous service of 5 years. Hence, the employee cannot claim their gratuity after 2 years of service.
NOTE: I don't have the terms and conditions of your appointment letter. Otherwise, I could have elaborated more. Hope this helps with your query.