The most likely error-prone addition is the most recent one: the resource converter. It is a component that should allow buildings to take in some resources and output other resources. It was designed along these lines of functionality:
- Input resources aren't consumed by buildings; they are still there to be, for example, traded away.
- Output resources are global; they can be connected to other cities and traded between civs.
- The number of functional buildings one can construct and operate depends on the availability of input resources. For example, if you have 3 coal and 2 iron, you can build 2 steel mills (each takes 1 coal and 1 iron as input, and outputs 1 steel); if then you trade away or lose (for example, in war) 1 iron, then one of these will stop, leaving you with only 1 steel produced.
- One input resource can be simultaneously used in several chains; for example, if you have one steel, you can use it to operate both an automobile factory AND a firearms plant.
There is at least one well-documented, if totally undefeated bug in the converter code now. As the game progresses, converter buildings start randomly turning off at the beginning of the turn, as if due to a resource shortage (when the resources are actually available); this effect seems to accumulate, and the further the game progresses, the more turn off messages there are. The buildings retain their functionality later the same turn (as they are still supplied with resources really), but this might be more than just a visual annoyance, especially as the effect accumulates, it might be causing CTDs. The trigger setting off individual shortage messages seems to randomly be ANY action modifying ANY resources - discovery of new resources, connection of new resources (even ones having nothing to do with any conversion whatsoever), trade between players.
Also, and this is likely connected to the first issue, sometimes at the beginning of the player's turn, any city production requiring ANY resource (once again, even not involved in conversion process, like horses) is discontinued as if due to the lack of resources. The player can manually resume the production after that the same turn (even as soon as he gets the message), since the supply of resource isn't actually broken.
Lastly, this likely also leads to CTDs late in game (must be some overflow happening). Players reportedly can avoid CTD in a save where it is otherwise unavoidable by declaring war on the most advanced AI civ (my explanation is that this leads to disruption of some trade deals).
Since the resource converter component is the latest developed, the process can easily be retraced through our SVN, which could help you do some reverse engineering, probably. There are many issues already fixed about it lately, but, since we no longer work with the guy who developed and fixed it, this is a work not finished.
All other components are pretty stable and well-tested. There can also be some (likely random) CTD due to better AI component, but other than that, most other stuff included has a long history of stable use.