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Thank you for your question. Can i please ask a little more information on what type of shake flasks are you using? Is it flat bottomed and has a loosened cap or is it a conical bottomed Bioreactor with a screw cap that possesses a hydrophobic membrane? The latter was designed to repel media upon contact with the cap during shaking and thus prevent media accumulation and the consequent risk of contamination. Alternatively are the flasks being reused via a cleaning and autoclaving methodology or is it a sterile unit opened in the hood every time. The latter may be the most popular route for time savings and convenience but more importantly to avoid any cross contamination.
Another thing is to possibly modulate is volume of shaking and speed of shaking if vigorous media sloshing is observed during the shaking duration; however your question stated that you are following proper protocol, so I would think that this point was already looked discussed and tested.