Should one inquire about the cost of a medical certificate that was not paid for previously due to an error on the part of the doctor or the center?

If it becomes clear that the non-collection of fees for the medical certificate was an error on the part of the employee, then you must pay the previous fees, unless the responsible administration pardons you and absolves you. The employee's error does not negate the right. However, if the administration pardons you or informs you that the certificate is free, then there is no blame upon you. The obligation is to free yourself from this right if it remains owing from you, based on the Prophet's (peace be upon him) saying: "Whoever has wronged another concerning his honor or anything else, let him seek his forgiveness today before there will be no dinar nor dirham."