I have submitted incorrect logbook information to SARS, what does that mean?

Unfortunately SARS will disallow the claim for milage unless you can prove via the logbook or if you can submit a detailed record of your travels splitting between business and personal travel. You don't have to worry, when you submit the other documents for review, leave out the logbook, SARS will disallow the deduction which will result in an increase in your tax payable.

Alternatively, change the ITR12 and remove the travel claim and resubmit

You won't get into any trouble this way.