Bonus as part of CTC
Including a bonus as part of the CTC is not incorrect. The company is not deducting it from your salary. Salary refers to the gross salary, and the bonus will be shown outside the gross salary along with other contributions payable by the employer, such as EPF, ESI (if any), or medical insurance premium.
In the monthly payslip, there will not be any mention of the bonus as a deduction from the salary. It is purely an amount paid over and above the monthly salary. As such, it is a cost to the company, which is why it is reflected in the CTC slip.