How to understand the first sentence as it seems to conflict with the sencond and third ones?
My people are wondering if you haven't identified secondary issues instead of the core issue. What about James opinion?Most people I've surveyed seem to think that is the answer.

It is about the identification of a company's core problem.
The second and third sentence seem to indicate that "you" haven't identified the core issue, but the first sentence seems to indicate that you "haven't" identified secondary issues, if so, don't they conflict with each other? Where do I go wrong? How to understand the first sentence?

Question

How to understand the first sentence as it seems to conflict with the sencond and third ones?
My people are wondering if you haven't identified secondary issues instead of the core issue. What about James opinion?Most people I've surveyed seem to think that is the answer.

It is about the identification of a company's core problem.
The second and third sentence seem to indicate that "you" haven't identified the core issue, but the first sentence seems to indicate that you "haven't" identified secondary issues, if so, don't they conflict with each other? Where do I go wrong? How to understand the first sentence?

Answer

Sorry to say this, but "wondering if you haven't identified" = "wondering if you have identified". There is a slight nuance difference, but they are essentially the same. So basically you have:
We think you've identified secondary issues.
What's James opinion?
Most people I've asked think you've identified secondary issues.