So how did this happen? Simple: The Minister claims to have never received the OGP's warning:
On 11 April 2016 I was first made aware of the Open Government Partnership Support Unit’s letter to the New Zealand Government dated 4 April 2016 (but received by New Zealand after that date). The letter dated 21 March 2016 referred to in your question was never received by the New Zealand Government.
"I didn't receive it" is the saddest of sad excuses, and it raises serious questions about whether SSC is fulfilling its duties as a point-of-contact competently. But also if they're paying this little attention to the issue then it explains a hell of a lot.
11 April is also when Bennett was briefed on SSC's plans to ignore the OGP's deadlines. Presumably, she also approved them. Which means when they turn into a clusterfuck and we get ejected from the OGP, we can hold her accountable for it.