comma after 'so' [conjunction]: time was 2 o'clock. So, I waited...

[learning_grenglish]

The bus arrival time was 2 o'clock. So I waited for the bus at the bus stop until then, when the bus arrived.

I have learned that we should use comma after a single word if it links the previous sentence. So, I think we do need comma after "So" which links the previous sentence. But the author haven't put comma, so I am confused. Could you tell me why it so?

 

[Thomas Tompion]

The bus arrival time was 2 o'clock. So I waited for the bus at the bus stop until then, when the bus arrived.

I have learned that we should use comma after a single word if it links the previous sentence. So, I think we do need comma after "So" which links the previous sentence. But the author haven't put comma, so I am confused. Could you tell me why it so?

You want to put the comma before so, not after it, Grenglish. The so explains something and you don't want to stop between telling people that an explanation in coming and giving them the explanation.

You use it correctly here:

But the author haven't hasn't put a comma, so I am confused.

 

[Arrius]

So is elliptical for and so where, I think you might agree there would be no comma. On reading the sentence aloud one does not pause between the so and I to which it is closely linked.
You have also written in red the comma after then, which I find to be correct, but I am not sure if you want an opinion on that.
Bear in mind that the English are not so strict about commas as, say, the Germans, and there is a general tendency on occasions to leave some out, although justified by grammatical rules, to prevent your text from looking as if it has small-pox.