Troubleshooting Thermostat Setpoint Not Met Hours (not exhaustive, but should get you started):

Run annual simulation
Request bin report for hours not met, or plot hourly values
Is this a morning warmup/cooldown problem or not?

Run design days (autosized equipment should meet setpoint on the design days that were used to size it)
Output setpoint not met variables
Output supply temperatures and setpoints
Is the supply air at the setpoint?
Does the setpoint agree with the design supply temperature specified in the sizing input?
If the supply temperature is at setpoint, then the flow rate is too small

If the supply temperature is not at setpoint, is the coil fully loaded?
If the coil is fully loaded, then the coil may be too small or the plant is not supplying enough
If the coil is not fully loaded, then there may be a control problem (setpoint manager, availability manager, components schedule)

If there is a central plant, are the plant loops at setpoint?
If the plant loop is not at setpoint, then is the boiler/chiller fully loaded?
If the boiler/chiller is fully loaded, then it may be too small.
If the boiler/chiller is not fully loaded, then there is a control problem (setpoint manager or equipment operation)