Zone exhaust fans and zone DOAS may cause this type of difference. The return node flow rate is equal to the sum of the zone supply inlet node flows minus the zone exhaust node flows.
I see where these numbers are coming from (i.e., the 25.243 inlet node flow and 20.460 supply node flow) however, what I don't understand is why this isn't happening all the time since the minimum OA flow is set to 25.243. I would suggest autosizing all the inputs or hardsizing them consistently. In your file the air loop is hard-sized throughout all the way to the terminal units where these are autosized. The total autosized flow rate for both terminal units is 20.46.
AirLoopHVAC,
AHU/L21/INT 1, !- Name
25.243, !- Design Supply Air Flow Rate {m3/s}
Fan:VariableVolume,
AHU/L21/INT 1 RAF, !- Name
NABERS HVAC, !- Availability Schedule Name
0.6045, !- Fan Total Efficiency
600, !- Pressure Rise {Pa}
25.243, !- Maximum Flow Rate {m3/s}
Component Sizing Information, Fan:VariableVolume, AHU/L21/INT 1 RAF, Design Size Maximum Flow Rate [m3/s], 20.46023
Component Sizing Information, Fan:VariableVolume, AHU/L21/INT 1 RAF, User-Specified Maximum Flow Rate [m3/s], 25.24300
Controller:OutdoorAir,
AHU/L21/INT 1 Outdoor Air System Controller, !- Name
AHU/L21/INT 1 Inlet pre HX, !- Actuator Node Name
25.243, !- Minimum Outdoor Air Flow Rate {m3/s}
25.243, !- Maximum Outdoor Air Flow Rate {m3/s}
Fan:VariableVolume,
AHU/L21/INT 1 SAF, !- Name
NABERS HVAC, !- Availability Schedule Name
0.6, !- Fan Total Efficiency
800, !- Pressure Rise {Pa}
25.243, !- Maximum Flow Rate {m3/s}
Component Sizing Information, Fan:VariableVolume, AHU/L21/INT 1 SAF, Design Size Maximum Flow Rate [m3/s], 20.46023
Component Sizing Information, Fan:VariableVolume, AHU/L21/INT 1 SAF, User-Specified Maximum Flow Rate [m3/s], 25.24300
AirTerminal:SingleDuct:VAV:NoReheat,
Thermal Zone: Level 14:INT 1:AHU/L21/INT 1 No Reheat, !- Name
Autosize, !- Maximum Air Flow Rate {m3/s}
AirTerminal:SingleDuct:VAV:NoReheat,
Thermal Zone: Level 30:INT 1:AHU/L21/INT 1 No Reheat, !- Name
Autosize, !- Maximum Air Flow Rate {m3/s}
Component Sizing Information, AirTerminal:SingleDuct:VAV:NoReheat, THERMAL ZONE: LEVEL 14:INT 1:AHU/L21/INT 1 NO REHEAT, Design Size Maximum Air Flow Rate [m3/s], 11.17615
Component Sizing Information, AirTerminal:SingleDuct:VAV:NoReheat, THERMAL ZONE: LEVEL 30:INT 1:AHU/L21/INT 1 NO REHEAT, Design Size Maximum Air Flow Rate [m3/s], 9.28408