The press release said that they had started the process of the transfer but it was never completed, it could very well be that NZF filled in some of the information but the person who needed to sign off on it couldn't be reached. In this made up scenario the Phoenix may have called, multiple times, and NZF may have told them that they were processing it and it would be done.
We have no idea.
The truth is that NZF knew that the transfer window was closing and that their only professional club was on the look out for players, hopefully the nix gave them a heads up that they were about to sign someone, but even so it was a critical time and one that happens only twice a year so they should have been on the alert.
The nix should have followed up, heck, they probably should have flown up to Auckland and sat behind the person who was entering the data into FIFA's system and not left NZF's office until it was done. But the fact is that the Phoenix has transferred dozens of players in the past and haven't had a issue like this before with NZF, so why would they start to worry?
They would worry because they have a lot to lose and the timeframes were tight. Anyone at a local club level awaiting a crucial transfer would have been on their back til it was confirmed.