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I think it just didn't end up working as well as scientists thought it would. Maybe there's more to painless nitrogen execution besides just filling a container with nitrogen. It's not like they can just test a nitrogen death chamber before rolling it out. We'll see if the next execution goes the same way or not.
Alabama did not listen to scientists. Medical science understands the roles of oxygen, carbon dioxide, and nitrogen quite well, and predicted that filling a mask with nitrogen would be a horrible application of the technology. The mask did not ventilate his own breathe, so the high concentrations of nitrogen did not displace the oxygen and carbon dioxide fast enough to avoid the gasping asphyxiation reflex.
There were specific recommendations made by scientists. Either use a mask with a one-way valve that exhausts exhalation, or fill a chamber of sufficient volume that will render the concentrations of his own exhalation insignificant. Alabama did neither, and it was a disaster.
I think the problem was that they didn't actually use a chamber and instead tried to use a mask, IIRC