It could also have been due to a confusion between metric and American units. The lowest airport on Earth as featured in the article is around 400 meters below

It could also have been due to a confusion between metric and American units. The lowest airport on Earth as featured in the article is around 400 meters below sea level, but the aircraft's software was designed to operate up to 400 feet below sea level. It's a rather odd limitation that can't be explained by "duh, they didn't account for negative numbers" alone.