Before I talk about my specific issue, I have to say that the GOLD version is one of the greatest games ever made. It ranks up there with Civ IV, Galactic Civ, Sins of a Solar Empire.

On the Phillip Campaign, I captured the city of "Scordisci."
Scordisci has 3 farms. The farms produce 35 food units each in the Autumn and 6 food units in the Early Spring.
I keep 2 "1st tribal javileers mercenaries" to quell the population. Each mercenary requires 6 food for a total of 12 units consumed.

3 Farms
If my math is correct, I should produce 105 in the Autumn and consume 12, for a net GAIN of 93.
In early Spring, 18 produced, 12 consumed. Net GAIN 6.

Yet, I am ALWAYS running out of food in this town even though the "Net Supply Transfer line" says POSITIVE 40.
This is problem ONE.
**********************
Potential bug 2.
After seeing that the 3 farms are FULL of food, it is apparent that the supply lines are not working. Even though all 3 farms are well within the "gold circle" So I clicked on the farm and right click on the city and the city fills up with food. I am only able to do this with 2 of the 3 farms. For the 3rd farm I get "no free supply node."
The potential bug here is that I shouldn't have to create a "supply node" since I'm within the golden circle.

For the first, yes there is a bit of wonkiness about the numbers sometimes showing an extra 0 at the end. Remember, during the winter the farms drop to 2 which maybe your issue there.
For the second, that is not a bug. The city you captured may have had only 3 nodes open. So you got one node used to connect with another city then a node used for each farm afterwards. Best bet would be to connect that remaining farm to a city close by that is close by (preferably the one connected to the city) to add the farm to the supply line. You can also try to upgrade the road to move more food from a full city to the one having issues.
Edit: Went and looked at the city. It has 4 nodes. Connect only one to a city and the rest to the farms. That way you can get the food into the supply line easier.

Ryat,
Thanks for your help.
Why do we need to use supply lines since the farms are within the "golden circle"
Truly it should be automated.
Also, the rule of 2 farms per city in the winter is silly.

The golden circle is for troops only. Farms need roads to the city. As for winter and farms only giving 2 food? Well not much is harvested during winter.

I guess these are game tweaks I would make when making a new version. And not actual bugs.
If the game developers do read this, then:
1. a. I highly recommend that any Farm inside the "golden circle" automatically be assigned to that particular city unless a trade route is opened directly from that farm to another city.
1b. If the Farm is given to the default city within the Golden Circle, then it should only count for 50% of a trade route.

2. I realize that not much happens in a farm in the winter, yet that is why the production rates go way down. Limiting a city to 2 farms in the winter seems arbitrary. Just my 2 cents.

Again, thanks for your help in the matter.