Unfortunately the doubling of building output in conquered cities was not the only bookkeeping error. I checked the numbers myself and they still don't add up correctly.
Case study: my current capital Copenhagen (see attached screenshot production.jpg).
Hammers:
It gets 20 hammers from buildings, 7 hammers from special buildings and 19 from worked tiles. Checking the map and buildings myself, these values confirm ok. This totals to 20+7+19 = 46 base hammers.
However, in the city base production is 48 hammers, and with a production bonus of 65% this totals 85 hammers. However, 48 hammers (which is already wrong) x 165% = 79.2 hammers, not 85.
Food:
It gets +18 from buildings, +3 from special buildings, +8 from worked tiles for a total of 29 food. However the screen total says 28 food.
I've included the save game as evidence.
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Investigating the causes.
Food: the culprit seems to be the Wild Herbs building. It gives +1 food from cooking, but this bonus is not added to the total food produced. Deleting the Wild Herbs building with CTRL-A does not change the total base food.
Hammers: the culprit seems to be the stone tool maker.
Copenhagen - stone tool maker test. Numbers are hammers produced.
start with recalc (shift-ctrl-T)
production: 48 base -> 85 total (bonus is 65%, from +25% buildings, +10% resources, +30% from civics) wrong bonus calculation, should be 48 * 165% = 79.2 . Also should be 46 base.
delete stone tool maker (5 hammer, 4 money, 5 science) with CTRL-A
result:
47 base -> 77 total (bonus: +25% buildings, +10% resources, +30% from civics) note: bonus calculation is now correct for 47 base. But 48 - 5 is not 47. And base should be 41 anyway
perform recalc with SHIFT-CTRL-T
result:
41 base -> 67 total (+25% buildings, +10% resources, +30% from civics) note: Base is now correct. bonus calculation is now correct.
Conclusion:
The stone tool maker which should give 5 base hammers secretly gives 7 base hammers. Aside and above from that it also gives way too much bonus. Based on +65% bonus that should give 7*0.65 = 4.55 bonus hammers for a total of 11.55 hammers. But instead it gives even more: 85-67=18 hammers.
Which corresponds with an hidden extra hammer bonus of (18 - 7 - 4.55)/48 = +13% of base production (including rounding errors).
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This is still very early in the game (just researched Sedentary Lifestyle) and
I have only investigated hammers and food, not money, science or other production.
Since I already found 3 bugs, there are likely more. A full audit of the
bookkeeping of all city production should be done but that is a time-consuming
project. Certain leader traits and possibly difficulty level also influence production
level, these should be included in such an audit.
Ok, I'm declaring this debugged. The first part of the problem was just a display miscalculation. The base was not being properly delivered.
The second part is more interesting. After a recalc with the stone tool maker still in place, you have the same base, 52 as you do before. (52 with 65% modifier equates to the correctly displayed 85 total.)
It's when the Stone Tool Maker is sold off that it gets strange. You get the correct -5 to the base bringing it down to 47 which seems correct initially. The modifier continues to correctly calculate the total.
However, when you recalc at this stage, you end up with 41 base (6 less).
Investigating further, if I add up by hand the base when I start the save, it totals to what appears to be 46. It shows 52 and after that initial recalc is still 52.
I have not been able to figure out quite how it totals to 52 rather than my count by hand of 46. BUT when I recalc, the 41 base makes sense at 41 because the 5 lost by the stone tools maker would reduce my hand count down to 41 from the original count of 46.
I couldn't figure out how this is taking place.
So that part of the equation is just... strange. But the first portion of the picture is fixed with a display repair.
EDIT: Further investigation...
I rebuild the Stone Tools Maker and the base goes back up to the correct tally of 46.
Conclusion: The recalc doesn't catch and repair the initial error that is still in place when the first recalc is run. It's not a problem with the building itself at all but with something to do with the assets until whatever the problem is is jiggled free by deleting the stone tools maker and recalculating.
Whatever this could be is a true mystery indeed but may not be something that continues to impact games as time goes on from here. However, the deletion likely clears some caching that allows the problem to truly be resolved.
Anyhow, if you want to watch carefully and keep doing the math by hand every round you may well find the moment this becomes a problem. (Maybe there's a temporary modifier taking place here like from a hunt or something too.) But as it stands I think the primary bug is resolved.
I'll be posting the update to the SVN shortly.
. This is one of those flow on effects I was talking about. They can fly into lake terrain so it is likely they can't fly into any of the surrounding terrain. 
, it might have been related to me deleting some lines in the water plane xml that seemed to have no effect on the game.
