I try to keep a list of reported bugs, which I update roughly monthly.
Here is the list for the time since patch k ws released:
http://forums.civfanatics.com/showthread.php?t=353687
Here is a list for items before patch k:
http://forums.civfanatics.com/showthread.php?t=329991
The general rule that I use is to delete nations in the worldbuilder, essentially with a manually applied binary search. If you can find that eliminating a nation resolves the bug, then you delete smaller parts of that nation, usually a manual binary pattern on cities. At that point, you can usually focus on nearby units. So start eliminating stacks nearby to see if you can find which unit is the culprit.
Unfortunately, for me the hardest part is finding which unit is the cause once I've localized the problem - this can take very long. On earlier versions, many WoC's were caused by the interaction of hidden nationaility units and 'regular' units. Hidden nationality (HN) is different from hidden. A hidden nationality unit can be controlled by a player, but appears to enemy untis as a barbarian unit. There are complex rules that don't allow HN and regular units to 'group'. For instance, an HN unit cannot go on a 'regular' ship. This kind of coding is complex and appears to have lead to a lot of WoC's.
For instance, before patch K, by far the majority of crashes and WoC's came from units with animal AI with hidden nationality (tigers, hill giants, etc.). However, there were other causes.
Hidden units may be even more complex. It is illegal for units at war to be in the same square, but this doesn't apply to hidden units; a hidden unit can be in the same square as an enemy unit. But then if the hidden unit is revealed, the code has to ensure that enemy units aren't in the same square, and if the code has some loopholes crashes will occur.
Hidden and hidden nationality units have been a major source of crashes and WoC's over time, but we have had and probably will continue to have some that get introduced in new releases.
Like most skills, those of us who fix files often start developing an 'eye' for what to look out for.
Unfortunately, we have had some very bizarre and complex issues since patch k. The best way to see what is likely to cause crahses is to read through the bug list and learn from other people's experience.
I hope this explanation helps.
Best wishes,
Breunor