Hi @jacob-fisher,
So you are saying that you have this situation:
In FusionAuth, a user user@example.com
In salesforce, a user user@example.com.
You configure salesforce to use FusionAuth as the source of identity, so there's a Login with FusionAuth button on salesforce.
When you try to log into salesforce in an incognito window, you see a new saleforce user with the email address user@example.com created (so now there are two)?
What are the two user ids? It's possible there is a mismatch and you might need to adjust the apex code.
Is that correct?