Although additional information is required pertaining directly to the 3 month contract I will attempt to advise as thoroughly as I can.
Fix term contracts has the definition as: as a contract of employment that terminates on –
(a) the occurrence of a specified event;
(b) the completion of a specified task or project; or
(c) a fixed date other than an employee’s normal or agreed retirement age.
The fact that the employee continued his employment well beyond 3 months, works for another person/render a service, in essence makes the employee a permanent employee, in terms of the basic employment conditions Act 1997 (Amended) S 83A the employee remain to have the status of an employee and the onus is on the employer to proof otherwise.
It is also true that even though the employer may or may not consider the employee as a temporally employee (reasons unknown) a person employed on a fixed term contract for longer than 3 months, may not be treated less favourably than someone employed on a permanent basis performing the same or similar work, thus meaning that the employee will be entitled to leave as described within the Basic conditions of employment contract.
The RIGHT to leave is not something that the employer may withhold and/or deny without justifiable cause, You should consult the Basic Employment Conditions Act at Section 27 for more clarity on your current situation and merits.
An Employer may not deduct any monies from the salary of an employee accept in accordance with Section 34 of the Basic Conditions of Employment Act, your attention is drawn upon the fact that unpaid leave can occur should the employee exhorted his leave and family responsibility leave in terms of the above sections, but the merits of each case should be weight upon what the law consider just and fair.
Kindly consider the above points and revert on the forum should require additional information.