Hi Gabriel,
To answer your question directly, and literally, what usually happens is that the conformity is still marked as "OK", and any necessary action is taken "outside of the system". That's because...
What SHOULD happen is that the conformity check is marked as "NG" and the descrepancy is indicated (in the NCTS IE44 message) with quite complicated rules and restrictions. Then the authorities get involved to resolve and agree the responsibilities and actions. All quite messy.
If you have access to the Europa web-site, you can find the "Transit Manual" in the Taxation & Customs area - let me know if you need the link (not to hand right now).
Regards,
Dave