If I unknowingly broke the law then its not the courts fault that I didn't know it, the onus is on me to know the law. They may go lenient on me because I didn't know what I was doing was illegal, but I still broke the law.
It is not quite like that, it is widely known that 'ignorance of the law is no excuse' and this is probably what you have based your comment on. However there are 2 elements to an offence, the mens rea [guilty knowledge] and actus reas [guilty action]. Both elements need to be present for someone to be guilty, unless the offence is one of strict liability. No guilty knowledge in something like theft or murder or assault would not fly as a defence because it would be reasonable for everyone to know that is wrong even if they do not know the actual statute they have broken. But in a situation where you commit an act and with an honest and reasonable belief that that act was not illegal – you have a defence.
This is a very generous interpretation. NZF don't exist in a vacuum, and moreover actively commit themselves to abide by FIFA regulations for tournaments NZF chooses to participate in (which in themselves stipulate that participating member associations undertake to comply with the FIFA statutes on player eligibility).
The onus is on the member association to ensure that they're compliant when they enter into the agreement to participate in a given tournament - and if they're not sure, to seek clarification from the governing body.
A common every day parallel for this would be speeding - if you get caught speeding, you don't have a valid defence by saying 'I didn't know what the speed limit was'. The speed limit is sign-posted and known, and the onus is on you as the driver to comply. Some people get away with speeding because strict enforcement on every day basis isn't feasible, so the onus is on drivers to comply with the regulations. If they don't comply and get caught, then that's it - you can't say 'oh, but I didn't know', or 'the guy in front of me was driving just as fast'.