Hey guys,
This from the help file:
"If the Quality level is displayed in Yellow, it indicates that the unit’s morale is reduced for some reason such as fatigue or ammo level. "
It was in the Hex Info Area section, describing what you see there. In addition to fatigue and ammo low I believe enfilade fire will cause it, and also (I believe) if you are using the "Flank Morale Modifier" optional rule, and you don't have support troops on the flank then this could change the color as well.