You are correct that you do not need to pay tax as you are below the threshold, however unless you have a directive saying that no tax should be withheld the company is obliged to do so and pay it over to SARS. The good news is that you should be able to claim all that tax back by submitting your ITR12.
If you are registered for eFiling you will be able to submit your ITR12 tax return as this should be on the system already. Alternatively if you have your IRP5, which you should have received from your regular client, you can go through the TaxTim process and insert your details and let Tim help you file your return.
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