Look, this is a simple situation. The OP requested that he's bill be limited to the inclusive airtime that comes with the contract. MTN has agreed, and in a round about sort of way, has done something or acknowledge this by updating the contract name on his monthly invoice....
Now, and TopUp contract is self explanatory. Once the inclusive airtime has been used up, the contract then converts over to prepaid for the remainder of the month. Go to any MTN branch, even call them and they'll tell you the same thing. It's not an OPEN contract where you get x amount of airtime, and when that finishes, you get billed at reduced rates. That would fall under an AnyTime contract. However, a TopUp feature can be added to that contract aswell..... So, back on track here, if on the OP's invoice, it says that he is on a TopUp contract, and still gets billed for usage out of the contract limits, then it's a fault of the SP, and the OP is technically not liable for those charges. Yes, one can argue that the OP should have been wiser to check the available airtime had he noticed that he can just call and there seems to be no end in sight... remember, with the R100 free airtime you get, it only gives you 42minutes of talk time should you only make a calls with the airtime. If you send an sms, or go surfing, that then reduces the mount of talk time you get. Now, if MTN persist with wanting to charge him for their incompetence, the OP can technically lay a criminal charge of Misrepresentation again the MTN group for what they are doing..... So in technical terms, MTN either has to credit his account with what he overpaid, or they can refund him. You must remember, it's a 2-way street, if a SP can take legal actions against you, then you can do the same to them if they are in the wrong...
I've had many contracts with them, enough to know how exactly they work, and the best people to speak to should you call them for anything. You sort of have to spoon feed them, and even if you just change the spelling of your name of the invoice, you must always request them to send you written proof that it is done. In this case, should they not send you proof that it is done, you hold back any payments due to them untill you get what you want(trust me, after a few calls to tell them that you holding back payment, they actually do send you whatever they need to).... In this case, it's not wise to do that now, as you have to do this from the start...
Just my opinion, feel free to comment should you feel the need....