Newer, improved high pressure common rail diesel engines require increased protection from damaging particles in fuel, resulting in tighter, low-micron filtration requirements. The unobstructed flow of fuel through filters underlies the well-known efficiencies and reduced exhaust emissions of diesel engines, and when flows are hindered, these efficiencies become severely compromised. Biodiesel fuels frequently contain saturated monoglycerides, glycerol (GLY) and/or steryl glucosides, systemic impurities that become problematic when low concentrations exceed ill-defined solubility limits, usually unexpectedly at low temperatures. Here, filters and blended fuels from seven flow obstruction incidents were subjected to detailed compositional analyses. With one exception the fuels contain estimated levels within international specifications, yet exhibit heterophase (HP) formation in the laboratory at 2 C, well above measured cloud points. Feedstock composition, pretreatment and/or purification processes are found to modulate insolubility risks. Interferences in standard gas chromatography methods used without modification can hide or complicate estimates of residual levels of GLY. The data show that classical variables controlling solubility, such as concentrations and temperatures, play important roles in setting the risks associated with in situ formation of HPs from these common impurities. Further, such risks are likely attenuated considerably by reductions in critical impurities beyond currently specified limits.