If a nickname or shortened name is generally used, then I would assume that the boss was using their full name for a specific purpose. It might not be that the employee is in trouble, it might just be that a higher-ranking boss is in attendance so the boss is trying to look professional by using full names.
However, I can see how it can seem as if there is a problem because (in the UK, at least) that assumption works for the relationship between a child and its parents. Parents usually call their children by their first name, or a contraction of it, but when the child is in trouble, they might use the full name.
Mum: Suzie, stop doing that.
Suzie: But mum, I like it.
Mum: Suzie, I said stop doing it.
Mum: Suzanne Louise Shepherd, stop doing that right now!!!
The words and the tone of the last sentence will tell the child that her mum is serious and that she is about to be in real trouble if she doesn't stop.
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