Burst
Chieftain
Hmm, I was suspecting the Aquifer, but if it is the feature then the yields should return to normal after it's removed (and you said they sometimes persisted) which means it might be a bigger issue.
The next time you play test, could you also try loading my Garamantes mod. They don't actually have to be a civ in the game, but just have the mod loaded alongside the rest. I seem to recall I might have fixed a similar problem for them (in which case, if its loaded, the fix should carry over).
Sure. Pleased to say that with v43 of The Garamantes active, Terrace Farms appear to be working properly and not affecting terrain yields.