Why is it in the morning but at night?

It is one of the exceptions. Learn at night as a fixed phrase, and in the morning, in the afternoon, in the evening as a set.

Do I say in the bus or on the bus?

On the bus, on the train, on a plane. Use in for a car or a taxi.

Grammar, compared

Think small to large. At is a point, on is a surface or a day, in is a space or a longer period.

In, on and at for time and place
Type	At	On	In
Time	Clock times, night, noon: at 5, at night	Days and dates: on Monday, on 5 May	Months, years, seasons, parts of the day: in July, in 2025, in the morning
Place	A point: at the door, at work, at home	A surface or a line: on the table, on the wall, on the second floor	Inside: in the kitchen, in Buenos Aires, in a car
Transport	A stop or station: at the bus stop	Larger vehicles: on the bus, on a plane, on foot	Small vehicles: in a car, in a taxi

1
Ask what it is
A point in time or space, a surface or day, or an area or period.
2
Match the size
Point is at. Surface and day is on. Area and long period is in.
3
Learn the exceptions
At night, at the weekend, on the bus, in a taxi.

En covers all three, so English needs a choice: en la mañana is in the morning, en la noche is at night, el lunes is on Monday.
Spanish has no preposition before a day: el lunes. English needs on Monday.
Say at home and at work, not in home or in work.
The weekend is at the weekend in British English and on the weekend in American English. Never in the weekend.

Why is it in the morning but at night?: It is one of the exceptions. Learn at night as a fixed phrase, and in the morning, in the afternoon, in the evening as a set.
Do I say in the bus or on the bus?: On the bus, on the train, on a plane. Use in for a car or a taxi.

Book a trial class. She writes back with times in Buenos Aires time.