Not sure if this applies, but I am used to seeing air bubbles on perfectly running VW diesels through the clear feed line. I think I remember someone saying it had to do with the filter? I thought it was strange, but they assured me it didn't make much difference, as the pressure is after the pump.
It does make a difference. It is true the pressure is after the pump.. but those air bubbles are still being sucked in to the pump.. The fuel that comes out of the pump has to cycle through the injector lines and back through the return lines. Air in the system will cause "misfiring" and smoke as the bubbles affect the popping pressures of the injectors. The engines you saw were not perfectly running then
well I guess it depends on the amount of bubbles really... one or two minuscule ones are probably expected, but big ones or frequent ones will cause side effects. It could be the filter, or it could be a connection way back at the tank that is slowly leaking in air as the pump sucks fuel through it, and air being lighter it will suck in easily.