has/had

She had learnt a lesson.

We use the past perfect tense when two events both happened in the past, and we need to make clear which one happened first.

Shirley had learned a lesson, then she apologised to her mother.

Incidentally, I think these sentences could be improved.

Shirley apologised to her mother for not sticking close to her. This caused her to be separated from her mother when they were shopping in a crowded shopping centre.[/B]

This suggests that Shirley's apology caused her to become separated.

I would rewrite it thus:-

Shirley apologised to her mother. She had not stuck close to her in a crowded shopping centre, and this caused them to become separated.

(Not only was Shirley separated from her mother, Shirley's mother was separated from her. They were separated from each other.)

Finally, beware! Many American English speakers find such British English spellings as "learnt", "spelt", etc, odd, quaint and old fashioned and insist on "spelled", "learned", etc.

Thanks.