Well... rosin core flux is pretty much pine tree sap with additives. Sticky and I imagine it could support mold growth. But I have never seen flux mold before. We have bottles of flux that are years old with no mold. They do dry out over a long period, though.
Typically add flux during rework - makes reflow easier. Used to use flux to remove SMT components but now use ChipQuick.
And splurge a bit - go to 63/37 solder. That small difference in ratio between 63/37 and 60/40 makes a big difference in reducing bad solder joints.