Hello
1. This morning most of the students arrived at school fifteen minutes after the lesson had begun.
2. The traffic was terrible, so by the time we arrived at the airport, our flight had left.
3. When we met I had a strange feeling I had seen him somewhere else.
I would use the past perfect in all of them, however I'm wondering if this would also be fine to use the past simple in the first one, i.e., ..the lesson began? Would you change something?