Terms of Employment: Working Hour Rates Payment

I would like and advice on the following Terms of Employment.

Is it legal for a company to pay employees as they please diverting from the contract signed between an employee and that company? The contracts mentions that you are to be payed for all hours worked. This is what has been happening with Truworths in Johannesburg, especially in Clearwater and Craddlestone Malls. Flexi Hours Workers, would work (for example based on the actual occurrence) hours that will be estimated to 4500 and they are only paid 3000. When the Store Manager was approached, she was not in the mood, and there is nothing she can do, that's the response. Holiday and weekend rates are paid as normal office hours, is this legal? A sick note from a Government Clinic is not accepted only from the one from a private Doctor is accepted, is this legal? We are talking about people from the Townships were a person with no medical aid but provided a Local Clinic by the government. And if any kind of the medical certificate is brought as proof of sickness you are given a warning??

This has been going on for long. The needs to stop, our people that are desperate to keep their jobs regardless of the treatment. They are afraid to stand up for themselves because once they do they are given 1minute late warnings and other unreasonable warnings until they have a solid reason to chase you them out. One will be acting Supervisor, and yet they have no chance of applying with the other Stores because of the warnings mentioned above, and now she/he's stuck with acting with no compensation because she/he is told that her/his record is not favorable for promotion, without being able to apply for the position else where or with them. I am deeply concerned on what is going on at Truworths and would like some advice.