I think your example is not a counterfactual, because in your world, landing gear actually didn't retract. Remember, whether something is counterfactual or not depends on what the facts are.

Had the landing gear been retracted in your hypothetical world, then it would be a counterfactual, but it probably wouldn't arise because it's not something out of ordinary - the landing gear retracting is a usual procedure. I think humans are more prone to make the mistake that is described in the article (stopping to search for the root cause) when they see a counterfactual conditional which premise is, in the factual, a procedural error (for example, "operator failed to monitor the disk space"). We see an error and mistake it for the root cause.