Quick update on current development: I am currently scouring the game for some long standing errors that can only possibly discovered by running a debug DLL. That's quite tedious because I concluded the most likely approach to finding them is to run a full autoplay with debug enabled, and that takes a while due to the performance cost of running the debugger.
It has already produced some success, however. I discovered and fixed (hopefully completely) the cause of bugs around culture that have been repeatedly reported, in particular with negative tile/city culture and weird consequent side effects. I also fixed some less critical bugs along the way.
A bug that I am convinced is real, but haven't been able to reproduce yet is the commerce inconsistency bug. I have seen proof of it in action though. What can happen is that the commerce (culture, gold, science, espionage) a specialist is "worth" when being added is different than when it is being removed. In particular, this can drive the output of a particular commerce of a city into the negatives or worse zero, making a division by zero error and crash possible. It also seems as if this error is located in cities only, not affecting the player owning those cities. This is good in principle, but can also be a problem in some calculations where those two values are assumed to be equal, leading to more potential division by zero crashes.
I will try to run more games to run into this error, and try more combinations manually. Please also keep your eye out for this. If you find a situation where that's the case, a save still helps. There is still the warning message appearing in the interface to alert you to this problem. When you see it, please immediately send me an autosave of the previous turn that did not have that warning.