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Can you clarify what EnergyPlus version you are using to simulate the .idfs on the DOE website?

One consideration is that the default files do not include an OutputControl:ReportingTolerances object, which specifies the temperature tolerance reporting for unmet hours. The default value is 0.2 deltaC, 0.36 deltaF, which a very tight tolerance.

Simulating the 90.1-2010 Large Office in Buffalo in EnergyPlus version 8.2.0 I get these unmet hours: default 0.2 deltaC / 0.36 deltaF tolerance: 286 occupied unmet hours heating, 677.5 occupied unmet hours cooling more appropriate 0.555 deltaC / 1 deltaF tolerance: 185.25 occupied unmet hours heating, 286.25 occupied unmet hours cooling

Another consideration is that EnergyPlus reports occupied unmet hours if there is any occupancy in the zone, and many schedules shut the HVAC system off below 5% or 10% occupancy. So these get reported as occupied unmet hours even though the HVAC system is intended to be off.

In general, unmet hours <300 hours is acceptable - though it's always good to check how far of the zone is from setpoint.

For more information on the DOE prototype buildings, see the answer to this question about the DOE Prototype buildings.