Something that I noticed while creating a assassin that primarily does poison damage, is that general vulnerability and physical vulnerability stacks do not stack with each other and further increase the poison damage done on any enemies that I hit. Each vulnerability type seems to work independently, just not together. Essentially an enemy that has 10 general vulnerability stacks will take the same amount of damage as the same type of enemy that has 10 physical vulnerability stacks or both 10 general and 10 physical vulnerability stacks.
Testing this on my other assassin that does flat heat damage, she did significantly more damage against enemies using both 10 stacks of general and 10 stacks of heat vulnerability than she did using just 10 stacks of either vulnerability separately, all other things being equal.
The only variable between the two of them which may be affecting this might be the psalm code doctrine [vulnerability stacks are +300% more effective for DoT effects]. The doctrine seems to work, but I'm not sure if it bugged in such a way to cause the different vulnerability stacking problems that I'm experiencing. I've tried playing without the doctrine, but the results have been inconsistent so far. If anybody knows anything about this, feel free to post about it.
EDIT/SUMMARY: Vulnerabilities are not meant to stack with each other, but still count as separate debuff stacks for the use of other abilities.