When running a merge action with a sublist (where related records are displayed in a table for each parent record, ie: A document based on Account, with list of opportunities in a table displayed in that document) you may find that the order of records in your sublist does not match the order of records from the data source (ie: report) that is feeding that sublist.
The default order of an Apsona report is set by the leftmost column and is in ascending order. You can consider adding a different sort and order in the "sort order" tab of the sublist report. You can also consider adding sort and ordering in the Sublist mapping area: