A deferral is a deferral is a deferral.
Until you hit a limit:
402(g)
ADP Test failure threshold for an HCE
Plan-imposed deferral limit
415
Then, if the participant is 50 years or older at any time during the year, up to $6,000 (for 2016) can be considered "catch-up."
Anything above those amounts, are treated as an excess pertaining to whatever limit they exceeded.
By "system" do you mean a payroll program? Or is it the record keeper's software? Or the TPA's software?