According to the mod description:

" !Attack of the Resistance Clones! - if the character pool is allowed to be used and a small enough pool is in effect, it may spawn already dead or active soldiers as resistance fighters in Haven Siege and Rioting City Extractions.

This can be disabled in the XComHavenSiege.ini with OverridePool set to true. "

Yes that's right.
If you have your character pool set to use saved characters then the mod will make resistance fighters from them.
So you either have random only set in your character pool, which isn't ideal if you have saved characters, or better still do the instruction above.

Originally posted by Alex F:

According to the mod description:

" !Attack of the Resistance Clones! - if the character pool is allowed to be used and a small enough pool is in effect, it may spawn already dead or active soldiers as resistance fighters in Haven Siege and Rioting City Extractions.

This can be disabled in the XComHavenSiege.ini with OverridePool set to true. "

Does changing this option disable pool characters in both haven siege and rioting city extractions?

Yes, no characters created or saved in the pool will be used.
Only random made up rookies will be used.

Where is this ini located?

It should be:
"C:\Program Files (x86)\Steam\steamapps\workshop\content\268500\647242867\Config\XComHavenSiege.ini"

The OverridePool function is at the top.

Does that ini file get reset every time the mod updates?
I've changed mine to "true" to avoid getting duplicates three times now. It fixes it briefly but then a short time later it happens again and when I go back to the ini file it's changed back to "false" again.

Yes it will, you have to make the change every time the mod gets updated.
I don't know why the mod author doesn't make it true by default as this is the best option.