We consider a 1% error ratio acceptable for our branches. But we have a 0% error ratio for the actual CTRs that are filed to FinCEN.
I agree, I caught many errors. We used two aggregation methods and they didn't always agree, so I would investigate and find which was right, make the correction and make note of it in case there were questions later. As long as the errors are caught before they leave the bank, I don't think they should count as true errors.