It is understandable that total particle count at the powder dispensing area is higher due to the reason you mentioned.
You should understand the behaviour of the total particle count to establish effective alert/control limits so that you are able to truly know when there is an abnormal situation that is causing additional variability that needs to be controlled. In other words… you must claculate alert/action levels according to the actual variability of your process, which for obvious reasons will be higher than traditional specs.
This should be understood and very well documented though, using a risk approach to the quality of the product and safety of the patient.
Taken from PIC/S Annex 1 (GUIDE TO GOOD MANUFACTURING PRACTICE FOR MEDICINAL PRODUCTS ANNEXES):
9.20 In the case where contaminants are present due to the processes involved and would potentially damage the particle counter or present a hazard (e.g. live organisms, powdery products and radiation hazards), the frequency and strategy employed should be such as to assure the environmental classification both prior to and post exposure to the risk. An increase in viable particle monitoring should be considered to ensure comprehensive monitoring of the process. Additionally, monitoring should be performed during simulated operations. Such operations should be performed at appropriate intervals. The approach should be defined in the CCS
I hope this helps!