Multiple Set-Cookie in header? Session regenerating maybe?

We have an issue with our simplesamlphp authentication.


I believe the issue is that the session is being regenerated.
In the Header I can see the following

Code:

Set-Cookie: ci_session=1f8a5fc76b261172fc190f8161cbc91ad5901b49; path=/; HttpOnly
Set-Cookie: ci_session=ea7e04c4099d5d5c217725c1a73caed5; path=/; HttpOnly

We didn't have this issue before. So I tried retracing back to what was changed. The only thing I could find is our upgrade from CodeIgniter 2 to CodeIgniter 3. 

When does CodeIgniter Set-Cookie multiple times?

This is my Cookie at the moment it happens.

Code:

Cookie: ci_session=1f8a5fc76b261172fc190f8161cbc91ad5901b49

So it looks like it's resetting my cookie and then resetting to a new one? I don't understand what is going on.