Part of the confusion is likely due to there being multiple sets of duplicates in the family. I went through and marked all the ones that looked like duplicates as Unmerged Matches.
Another confusion point is Petie-6 is shown with father William Petrie-1570 and with mother Elizabeth (Holmes) Petie (Holmes-15841), while her "sister", Elizabeth Holmes Petrie-1568 is shown with father James Petrie-1582. It appears that James should be the son of William.
I would suggest laying out the generations on paper to see father, mother, child, spouse, etc., so you can see which is the correct lineage. Then, I'd recommend merging the ones that are clear matches, merging to the correct name (Petrie vs Petie..?)