The intent to proceed rule is not the issue. If you failed to provide the consumer an LE, regardless if it's a "technical" issue, then you did not comply with 1026.19(e) for providing a good faith estimate for the charges. Since you did not disclosed any fees on a LE to compare the CD fees to you have tolerance violations. 10% of 0 is 0 and then there are the 0 tolerance charges.
You owe the consumer a cure for the closing costs.