FinCEN has never offered any guidance on whether an error must be "material" before the filing of a correction is necessary. Any advice you get here that involves anything less than correcting all of them is going to be based on a personal opinion which your examiner may not share. I suggest you call FinCEN for advice at (800) 949-2732 and document the conversation. (You could call the IRS Hotline at (800) 800-2877, but I am more and more frequently told they do not call back with any degree of predictability.)
Measure the depth of the problem by comparing the number of CTRs with mistakes to the number of CTRs filed by that branch. The variety of errors you describe is more easily attributable to sloppiness than poor training. There is also something wrong with your internal controls, the errors should have been detected by the person who reviewed the forms prior to filing. Before you implement remedial training, check the CTRs filed by a couple other branches to see how widespread the problem might be.
In the interim, i.e. right now, tighten your internal controls to stop the bleeding. Annonounce that all CTRs will be thoroughly reviewed before filing. Any that are incorrect or incomplete will be sent back to the preparer. Repeated errors will result in disciplinary action. In my experience, the single greatest improvement you can make in quality is to tell people their work will be reviewed by others.
Obviously, the end result is to retrain the personnel involved.