This issue sounds like a mysterious one, but it could very well happen due to a manual mistake or system issue. For Smartbridge, it happened on a recent project when our client chose to upgrade from JD Edwards EnterpriseOne Tools Release 9.0 to 9.2.
During the project, the data selection for the custom versions of Payroll Driver (R07250) messed up when we promoted it to Tools Release 9.2. The final update, which was the last step in the payroll cycle, selected the records multiple times and processed them repeatedly. When we reviewed the logs, we identified the primary key issues, but did not suspect the data selection itself to be the driver of the problem. After two weeks, we finally realized that data selection was in fact causing the root issue.