But the charges against their parents were dismissed because there was no evidence to show Hotai and Schuster should have known the children needed medical care, as they did not have obvious injuries.
University of Otago faculty of law professor Mark Henaghan said shaken baby cases were particularly difficult to prosecute, given there were often no witnesses.
I know people feel angry and upset, but that's not your point to judge, it's not a political thing he's doing here, it's a judicial thing ...
"There's evidence worldwide that they have the lowest success, unfortunately, for prosecutions."
Issues included identifying who did the shaking, as well as when and why they did it.
"Without that sort of evidence you really haven't got much to go on to prosecute."
This case is complicated by the fact Schuster often disappeared from the family home for periods of time, leaving the babies in the care of various different friends and family members.
The injuries were discovered in April last year when Hotai awoke to find one of the babies had apparently fallen off the bed and was struggling to breathe. He admitted accidentally dropping her again while running to get help, but has not been charged over this.
Henaghan said there were a number of checks and balances in place to prevent cases going to court without sufficient evidence, including the ability of the judge to dismiss the charges.
There's no point prosecuting just to make a statement, because it's just a waste of everybody's time.
"[Justice Hobbs] is a very experienced judge. He's looking at the evidence. He knows from previous experience that on that sort of evidence it's not going to go far enough."
People who were unhappy with the decision to dismiss the charges did not have all the evidence, while Justice Hobbs did, Henaghan said.
"I know people feel angry and upset, but that's not your point to judge, it's not a political thing he's doing here, it's a judicial thing, and he has to look at the evidence and he has to make a careful decision based on the evidence and what's in front of him."
In his decision, Justice Hobbs said there was not enough evidence that a properly-directed jury could reasonably convict Hotai and Schuster of failing to provide care.
There is also no evidence to show who shook the babies, and nobody has been charged yet with causing the injuries.
"There's no point prosecuting just to make a statement, because it's just a waste of everybody's time," Henaghan said.
Detective Senior Sergeant Neil Holden of the Child Protection team encouraged anyone with information to come forward.
"The police Child Protection team endeavour to keep children safe, and consider success in a connected prosecution as an important, but secondary objective."
Police strive to get the best outcome for all parties, and this was aided by appropriate adult behaviour and "brave ownerships of issues by adults" so the wider situation can be addressed, he said.
"This may, or may not, involve prosecution."
The twins are no longer in the care of their parents.
