Some thoughts off the top of my head;
A good question that I'm sure your Ethics Committee (IRB/IEC) would be happy to help with. Obviously retrospective consent is not desirable, so there are several questions you should ask yourself.
Have you got an escalation process that raises these non-compliances? Do you have a process to analyse the route causes of these problems and put in place corrective and preventive plans to stop recurrence of similar problems in this site, at other sites, and in other trials (as required by the new draft ICH E6 R2 (step 2b))? How are you going to ensure that these potential problems are detected in future?

Is this a significant violation of the subjects rights? The new Clinical Trials Regulation 536/2014 Article 52 (an EU law already, but not yet in application), a breach of GCP "likely to affect to a significant degree the safety and rights of the subjects...."? Once the CTR is applied, it would be necessary to report to the regulators (via the EU Portal) any Serious Breach of subjects rights, within 7 days. However the new Clinical Trials Regulation 536/2014 does protect data already collected - "the withdrawal of the informed consent shall not affect the activities already carried out and the use of data obtained based on informed consent before its withdrawal" (A28.3).

We can see the sensitivity of the regulators from what they have written about the situation where consent no longer exists. Look at the MHRA paper on (2009) Guidance on the maintenance of regulatory compliance in laboratories that perform the analysis or evaluation of clinical trial samples - "all laboratory personnel that perform work in support of clinical trials must exercise due diligence to ensure that the work they have been contracted to conduct is covered by the consent given by the trial subjects" and "there should be a mechanism to ensure that the laboratory is informed in a timely manner if consent is withdrawn to ensure that no further data is generated or collected".
This MHRA guidance might have been superseded by the EMA "Reflection paper for laboratories that perform the analysis or evaluation of clinical trial samples" (2012). Look at the section regarding withdraw of consent and analysing samples.

Destroying sample is a sensitive situation and this would be a good question for your IRB/IEC as well as your organisations management.