Ford had a Technical Service Bulletin - 06-25-04 - that addressed water collecting in doors. The bulletin has you check the door drains to ensure they are flowing freely, and also trim a flange of the rocker seal at the bottom of the door for more flow.
RepairPal Certified shops can diagnose and repair your 2005 Ford Five Hundred. They provide transparent pricing with a minimum 12-month or 12,000-mile warranty on repairs and services.