I have searches that pull all transactions referencing certain sales orders. This is accomplished through a custom field on the header and on the line of transactions called "related SO". Originally I had this pulling mostly bills but I am now pulling lots of credit card transactions as well. Since I added those credit card transaction, when I run the search in Netsuite, it has one line per transaction (most of the transactions are only one line) as it had before, but when I export the search, it was returning multiple lines where it should only show one. I was going to create a support ticket and then I realized that it was repeating the transaction for the number of lines that are in the related SO it was referencing. In my Criteria, I had to add a mainline restriction on the related sales orders using the joined record main line field. Now the saved search and its export is showing only one line per transaction.
So even though the transaction it is searching cannot be mainline, because a field that is part of the criteria references a sales order, that mainline limit must be put on the those related so fields. Not intuitive at first. I hope this helps someone.