Any opinion on if it is permissible to include a late payment on the CD if the disclosure on page 3 of the LE was omitted by mistake?

My opinion is no - when they gave intent to proceed with the loan, they were under the impression that there would not be a late charge. It doesn't seem fair that because of a lender error that they'd now be subject to a late charge without any kind of product change.

There is no such guidance in the regulation. You have a disclosure violation on your LE. That is the extent of the damage.

Omitting the late payment information on TRID disclosures does not negate it's disclosure in the promissory note, which is the contractual source document used to demonstrate disclosure of the late payment amount and criteria.

Make sure you disclose it properly on the closing disclosure and determine why it was missed on the loan estimate. Fix the problem to prevent it from happening again.