why was aunt polly upset when tom skipped school the second time(after he go engaged to becky

Are you sure you have your chapters right here? Tom doesn't get engaged to Becky in Chapter 7, before Tom witnesses the murders and runs away to Jackson's island with the boys.

In Chapter 10, after the "engagement," Sid tells Aunt Polly about Tom's late night, and she lectures him about how he continually breaks her heart, spurring quite a bit of guilt on Tom's part. Tom sees her "heavy sorrow," as “worse than a thousand whippings.”

Excuse that first post........ I mistyped........... Tom gets engaged in Chapter 7