The differential pressure (dP) is the pressure lost due to friction as water passes through the system. You take a reading before the pressure vessels and after the pressure vessels of each stage, and that tells you how much pressure was lost across that stage.
A very high concentrate flow rate will result in a high dP because of the high friction. From a fouling perspective, scale, suspended solids, and biological growth, etc… build up in the feed channels and interfere with flow, thereby increasing friction and resulting in pressure losses.
If you are concerned about scale, then you should be monitoring your normalized permeate flow, not your dP. Monitoring normalized permeate flow allows you to detect scale formation and address it well before it is detectable by an increasing dP. Once your dP has increased, the scale will have already become very thick and will become more difficult to clean. The opposite is true for suspended solids, where you may see a significant increase in dP with minimal impact on normalized permeate flow.