The terms are relevant in other places (not just EMA). Internal failure costs are costs because of something going wrong before goods are delivered to the customer. External failure costs are costs after delivery to the customer.
In the context of EMA, internal failure costs would be things such as wastage and pollution in the factory. External failure costs would be things such as being forced by law to dispose of customers old fridges when the customer buys a new one as is the case in the EU.