Why is McCarthy v Smith [1979] not applicable in Factortame?

In McCarthy v Smith it was said:

Under s 2(1) and (4) of the European Communities Act 1972 the principles laid down in the treaty are ‘without further enactment’ to be given legal effect in the United Kingdom; and have priority over ‘any enactment passed or to be passed’ by our Parliament. If on close investigation it should appear our legislation is deficient or is inconsistent with Community law by some oversight of our draftsmen then it is our bounden duty to give priority to Community law. If the time should come when our Parliament deliberately passes an Act with the intention of repudiating the Treaty or any provision in it or intentionally of acting inconsistently with it and says so in express terms then I should have thought it would be the duty of our courts to follow the stature of our Parliament.

The legal issue on the Factortame litigation was that the Merchant Shipping Act of 1988 is contrary to the European Union (EU) law and as a result can not be imposed to the Spanish Fishermen as Spain joined the EEC in 1985. The Spanish fishermen requested that the High Court disapply the UK Act of Parliament. The court issued an injunction which temporarily suspended the Secretary of State for Transport from enforcing the Act. This issue was taken up by the Court of Appeals and later by the House of Lords (Regina v Secretary of State for Transport, Ex parte Factortame Ltd. And Others (No.2) [1990] which both confirmed that the decision of the first Court was wrong as the Courts did not have the power to suspend an Act of Parliament. The House of Lords were obliged under the European Union law to refer this matter to the European Court of Justice (European Court of Justice) which ruled that domestic courts were able to disapply a domestic law which contravened EU law and therefore the Merchant Shipping Act 1988 could not be applied.

Why is this? Why couldn't McCarthy v Smith be applied in this later case?

Because the Merchant Shipping Act 1988 wasn't passed 'with the intent of repudiating the treaty' nor did it say in express terms that parliament intended to act inconsistently with the treaty or any provision of it.