Good question.
Bus stops are small - you can't get into them, so at a bus stop, at the bus stop.
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I attend university = I am at university.
Where are you? I am on the university campus right now = I am at the university.
What do you do for a job? I am at the university.
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If the bus stop is a big building, you can be in it. Not a common thing to say.
I am at the train station = I am there.
I am in the train station = I am there, on the inside.
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He excelled.in school - during those years
She excelled.in university - during those years
She excelled at school
He excelled at university.