I accidently filed a CTR twice. Do I have to notify FinCen, or can I let it pass?

If you just filed it, sometimes you can contact them and get the submission cancelled, otherwise, once acknowledged there is nothing you can do about it, but document your review of controls and any procedural changes made so that it does not happen again.

You need to let them know you accidently filed the CTR twice. From the BSA E Filing Website:

"I accidentally submitted the same filing twice. How do I correct this?
For CTR/DEP/CTRCs filings, send correspondence to the FinCEN which includes the DCNs for the original and duplicate filings and state the DCN(s) to be removed.

Note: This process does not apply to SAR’s. Once filed, a filer may only correct or amend a SAR.

If you suspect, but are not sure that you have submitted a duplicate filing, contact the BSA E-Filing Help Desk at 1-866-346-9478 (option 1) or BSAEFilingHelp@fincen.gov. Provide as much information as possible and include your bank name and the filing date(s)."

Thank you both