When filing an Amended CTR on the BSA E-filing system it calls for a "Document Control Number (DCN)". What is that exactly? would that be the Tracking ID?

The DCN is the Document Control Number assigned by FinCEN once they received the original filing. It is not your internal tracking number.

So, this is something we should get from FinCEN? We internally found an error on a CTR though a routine audit, it wasn't something that FinCEN told us to fix.

After you file the CTR, you get a response back from FinCen that tells you the DCN. You need to save this so you can reference it if needed.

You can search for it by going through the link on the side of the site called "track my organization status". You can select your date range and find the filed CTR there with the DCN #

Any chance you filed the original CTR on paper? If so, you can stop looking, you do not have a DCN for it.