First thing I would do is change the flow rate goals from volume flow rate to mass flow rate. Volume can change with density, but mass does not.
If you are still having an discrepancy with mass flow rates, then there's definitely something wrong. Maybe you have vortices crossing your goal surfaces which are giving your wrong readings.
Give the following a try , this will ensure that Axial fans I'm assuming they are axial) behave in the correct manner within Flow Simulation
Fan Pressure Type - Pfa free blowing
REASON - This is because that although fan curves are written as static pressure, most normally the pressure difference is actually calculated using the total inlet pressure and outlet static pressure - this is what the free blowing pressure measures. It is easier to measure the total pressure at the inlet as it is approximately equal to the environment pressure in the suction chamber.
Fan Inlet Geometry - Simplify if possible , but make sure the area calculation is accurate
Fan Outlet Geometry - Simplify if possible , but make sure the area calculation is accurate
Initial Mesh Settings
Narrow Channel Refinement - 10 cells across a narrow channel (the default is normally 5)
REASON - This will help when the fan outlet is in close proximity to the walls (~ 1/2 Diameter)
Thin Wall Resolution - Turned ON
If using automatic grid settings define the min wall thickness and the min gap distance so that thin wall and narrow channel work correctly. Define them as the smallest dimension for the thin wall and gap that you are interested in, this will ensure the Narrow Channel Refinement and Thin Wall Resolution functions operate correctly.
Goals - Set goals for the fan - for a typical free blowing set the following
Surface goal for total pressure at inlet face
Surface goal for static at outlet face
Equation goal for Pfa equation goal using the above ( SG Av Static Outlet Pressure - SG Av Total Inlet Pressure )
Surface goals for volume flow rate and mass flow rate at relevant points, for easy checking once the model is solved.
Ensure that you check the mass balance in and out of the system ..... it should be the same (or as close as possible )
Hope this helps