Does primer normally separate in to different colors, or is this mold growing in it?
Primer-unbdercoat often has a higher pigment content than topcoat paint, this helps it cover marked surfaces better. usually the pigments are a combionation of carbon black and titanium oxide white.

When left to stand the different pigments will separate at different rates giving a mottled result like you show above.  just give it a really good stir. Not ten laps with a popsicle stick, a it'll take a really good stir to mix the settled pigment back into the resin.  I use a bent wire in an electric drill.