This is intended to be a summary post. Please make separate posts of unreported or new bugs in new threads with version information and if possible logging to make issues easy to track down. As these are resolved, I will remove them and add new issues as needed (we might sticky this so people know what is and isn't going on and Thal knows what hasn't been resolved).
Note: Having trade route income with just the capital is not a bug. This is now an intended feature in GEM that the capital can trade with itself (resolves the railroad connection capital bug as well).
Known issues:
1) Animations on created combat classes do not work. Fix requires core mod (or may not be possible.)
2) City yield tiles (the city square itself) on surrendered cities do not work. Vanilla bug. May require core mod or may not be possible. Workaround: don't accept cities in peace terms. Conquered (or re-conquered) cities should work normally. AI won't know to not do this though...
2a) Also impacts any opportunities on that city tile, so a second workaround is to never spend money on any opportunities that might improve that city tile. - Firaxis appears to have patched this in the March patch.
Bugs/issues as of 2-3-13:
1) City health resets to max 300 with no palace/walls hit point bonuses on reloading a save.May be vanilla bug but there wasn't a numbered city health bar before to confirm. Using IGE to remove defensive buildings lowers the hit points max below 300. The city health check appears to run once on loading and doesn't look for "extrahitpoints" modifiers at that time, sets them at 300 then. Extra hit points will add correctly as they are built or added in game via policies/wonders/new cities.
Update: Is a vanilla bug, resets city HP to 300 on load, may require core mod, or might be fixable. Still testing. The game does correctly add HP from buildings that add it when they are built/acquired naturally. I'm suspicious that this could be adapted to fix the problem in lua.
Update: Appears fixed in civup 2.6, Firaxis also patched this in March.
2) Building tooltips from beliefs do not appear on buildings. Do appear in city yields. Happiness does appear in top bar and economy summary.
2a) Additional food from tradition policy doesn't appear on walls, but does appear in city yield. Production from liberty tree does appear in both. (Disregard? Appeared to be working)
3) Faith yield in city incorrectly displays, does not count per population effects. Does work on mouseover. Does not work in economic summary or side bar. Faith from CS also appears to display in top bar incorrectly.
4) Feed the world belief counts 2x (adds 6 food per building)
5) Air repair and march both available to air units. Fixed in 1.4
6) Minor flavor issues with buildings/policies
-Stone Works has no happiness flavor.
-Merchant Navy should not add production flavor. Fixed in 1.4
-Furnace has no GP flavor (adds engineer slot).
-Seaport has no science flavor. Fixed in 1.4
-Unique buildings to be set with zero upkeep? (chinampa, burial tomb, paper maker, mud pyramid mosque)
7) Typos in building end.sql causing cost/upkeep adjustment errors.
-theater should be theatre
-smithy should be workshop
-workshop should be windmill Fixed in 1.4
8) Influence from "you have impressed us with culture/techs/faith" is back at 40. Intended?
9) City square food default is 2, not 3 as intended Fixed in 1.4
10) Capital gives no culture after city hall building was deleted. Palace previously granted +1
and +2 
, one or both could be restored.
11) Culture from CS counts twice (in cities and in top bar)
12) Commerce +15%
does not apply in an obvious way (adds only to net, which can mean very little extra gold). It does seem to correctly apply to any gold sources however (trade routes, religion, etc).
12a) Occasionally causes gold per turn to run negative? (unconfirmed, but my past experience with any crazy negative GPT error usually coincided with taking commerce).
13) Courthouse +3
in nationalism tree deleted (police state) and not replaced (populism)
14) Policy/belief/happiness status change effects do not take effect in UI until next turn.. It will update on entering a city screen. There's also a display glitch in between turns if the research UI is open. Research per turn will display there as a very small amount with a resulting high turn count, but this has no apparent effect on research times, and the top bar remains accurate. None of these appear to have game play effects, just reflect how quickly accurate information is available from significant changes.
15) Sistine Chapel doesn't add 25%
16) Tooltip on economy happiness screen displays incorrect # of unhappiness for cities and occupied populations. The displayed total is correct however.
17) Instant population on med labs/vaccines not triggered. Appears fixed in 1.4
Note: Having trade route income with just the capital is not a bug. This is now an intended feature in GEM that the capital can trade with itself (resolves the railroad connection capital bug as well).
Known issues:
1) Animations on created combat classes do not work. Fix requires core mod (or may not be possible.)
2) City yield tiles (the city square itself) on surrendered cities do not work. Vanilla bug. May require core mod or may not be possible. Workaround: don't accept cities in peace terms. Conquered (or re-conquered) cities should work normally. AI won't know to not do this though...
2a) Also impacts any opportunities on that city tile, so a second workaround is to never spend money on any opportunities that might improve that city tile. - Firaxis appears to have patched this in the March patch.
Bugs/issues as of 2-3-13:
1) City health resets to max 300 with no palace/walls hit point bonuses on reloading a save.
Update: Is a vanilla bug, resets city HP to 300 on load, may require core mod, or might be fixable. Still testing. The game does correctly add HP from buildings that add it when they are built/acquired naturally. I'm suspicious that this could be adapted to fix the problem in lua.
Update: Appears fixed in civup 2.6, Firaxis also patched this in March.
2) Building tooltips from beliefs do not appear on buildings. Do appear in city yields. Happiness does appear in top bar and economy summary.
3) Faith yield in city incorrectly displays, does not count per population effects. Does work on mouseover. Does not work in economic summary or side bar. Faith from CS also appears to display in top bar incorrectly.
4) Feed the world belief counts 2x (adds 6 food per building)
6) Minor flavor issues with buildings/policies
-Merchant Navy should not add production flavor.
-Furnace has no GP flavor (adds engineer slot).
-Unique buildings to be set with zero upkeep? (chinampa, burial tomb, paper maker, mud pyramid mosque)
-theater should be theatre
-smithy should be workshop
-workshop should be windmill
8) Influence from "you have impressed us with culture/techs/faith" is back at 40. Intended?
10) Capital gives no culture after city hall building was deleted. Palace previously granted +1
and +2 , one or both could be restored. 11) Culture from CS counts twice (in cities and in top bar)
12) Commerce +15%
does not apply in an obvious way (adds only to net, which can mean very little extra gold). It does seem to correctly apply to any gold sources however (trade routes, religion, etc). 12a) Occasionally causes gold per turn to run negative? (unconfirmed, but my past experience with any crazy negative GPT error usually coincided with taking commerce).
13) Courthouse +3
in nationalism tree deleted (police state) and not replaced (populism)14) Policy/belief/happiness status change effects do not take effect in UI until next turn.. It will update on entering a city screen. There's also a display glitch in between turns if the research UI is open. Research per turn will display there as a very small amount with a resulting high turn count, but this has no apparent effect on research times, and the top bar remains accurate. None of these appear to have game play effects, just reflect how quickly accurate information is available from significant changes.
15) Sistine Chapel doesn't add 25%
16) Tooltip on economy happiness screen displays incorrect # of unhappiness for cities and occupied populations. The displayed total is correct however.
or does it mean the tooltip was changed back to +2 on buildings and free buildings?
