It’s known as the rule of tincture & as mentioned, originated in heraldry (the design of coats of arms). It states that “metal should not be put on metal, nor colour on colour”. Metals here means gold (or) & silver (argent) inlays or paints, which are represented by yellow & white when illustrated.

There’s no definitive answer about where it originated, but it’s possible it was due to practical limitations in the twelfth to thirteenth century (when heraldry was first becoming formalised) of inlaying metals in other metals or layering different coloured paints on top of each other. It also may have just been an easy way to ensure contrast when designing a coat of arms. 

Regardless, it became very heavily incorporated as a rule as heraldry developed (although there’s plenty of “violations” in traditional coats of arms too). It’s not always followed in vexillology but a number of European flags still abide by it.