There are several explanations for why this discrepancy may occur.
Possibility #1. The employee who exists is a non-HRDB employee. The latest version of VEDs downloads employee data only from HRDB. Beacon HR now accesses the NED database to pull in information about contractors from your institute.
Possibility #2. In VEDs, the organization to which the employee was assigned was deleted from the user interface. The "orphaned" employee no longer displays in the VEDs interface. Beacon HR solution to "orphaned" employees is different from VEDs. Instead of excluding the employee from the interface, Beacon HR assigns this employee to a "not defined" organization and still lists the user in the interface.