also there are some bugs with shintoism buildings + agricultural trait, when i played all was ok, but when i load save i have big penalties to food, some wrong miscalculations maybe?
I came across the same (?) bug...

I had a long game session yesterday where i did not pay too much attention to everything as i was doing other stuff at the same time. All seemed fine, my cities had lots of food and grew a couple of times, so i allocated many specialists in every city to combat the fast growth...
After loading the save today i noticed that all my cities were starving, see attached savefile 1.
My leader has the agricultural trait and my civ has a state religion (Buddhism), although it is not spread to all cities yet.
As it turns out the problem is that after some time every city gets extra food, out of thin air it seems.
And i think it gets worse the longer you play the save, so you end up with a city which seems to have, say +2

, but is actually starving.
It looks like this in the city screen...
Try to play savefile 2 for a little bit and you should eventually notice the mysterious extra

after maybe 10-20 turns...sometimes it takes longer.
I did not see this happening when playing with other leaders, so i cannot say if it is just the agricultural trait or a combination with a certain civic,religion,building or action...
A force recalc did nothing, only reloading the savefile or restarting the game reverts everything back to normal, for a while at least.