Most airlines, especially the "legacies" AA, DL, UA and US, block certain seats/rows from pre-assignment and only allow agents or kiosks at the airport to assign them. This is, theoretically, so that a party traveling together or those who need designated "handicapped" seats can be accommodated however we've all heard how well that works, in theory.
Also bear in mind that airlines will usually "upgrade" their "elite/status" frequent fliers to the "premium" seats 24 hours prior to departure so its highly possible some of the empty seats were once held by a frequent flier who was moved up.
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