Yes,CNC is a segment where squaring off ( even intraday square off ) is not allowed. So whatever quantity you have sold has to be compulsorily delivered and all your buy trades will result in compulsory delivery with a proper pay in.The shares sold if not delivered, will get auctioned with penalty as it will be considered short delivery.
In CNC mode, you can't sell any extra qty that you don't own. So, there is no issue of short delivery there.
In MIS mode, if you sell most of the brokers will cover the position for you by 3:15. But, in case a lower circuit happens and no one is buying, you will end up paying penalty.