Dear Ali. The conceivable ...

Dear Ali. The conceivable reasons would be membrane fouling, piping joints blockage or non-original membranes. With assumption that the system is new and has been properly flushed before coming into service, the two other reasons remains.

My suggestion is checking system pressure drop after unloading all membranes. Then you would find out if any blockage is there.

Also checking individual membrane test in a dedicated pilot containing a single membrane PV and required indicators to see if there is any difference between actual test amounts and ones reported by the manufacturer.