TL;DR
1. Consider Ishikawa (“fish bone”) diagrams before applying the 5 whys or as a way to help organize the 5 why process.

2. To improve a system, first determine what is constraining the performance of the system. This is 80/20 thinking and attempting to optimize globally instead of locally. Local improvement may not result in system improvement.

Longer explanation and examples follow.

1:
The 5 whys are a great problem solving tool. Often there are many potential root causes which need to be investigated. Sometimes there is a single root cause that is responsible for the problem being investigated other times there are multiple factors that interact to cause the problem.

An Ishikawa or “fishbone” diagram is a useful tool to help organize many potential root causes.

In the example of pain and swelling caused by intubation we could start a little higher before diving into detailed 5 whys.

We can start with top level groups, such as:
- material
- method
- person
- patient

For each group, we determine potential root causes. This can be done through asking the experts performing the process, reviewing SOPs, observing the process, looking at process parameters, literature reviews.

Some examples, material could be the material of the tube, the type of coating being used, anesthesia, etc.

Method could be how the tube is inserted.

Person can be if the person is new to the process or experienced, is the person following procedures...

Patient could be if the patient has any allergies to materials or adverse reactions to medication or anesthetic...

The above are illustrative. You can decompose the groups in different ways. You can define the groups differently. Of course the above isn’t comprehensive or unique. Try to be MECE or mutually exclusive and collectively exhaustive when decomposing the problem space.

We often try to investigate the potential root causes by performing statistical experiments to try and determine cause and effect and which variables significantly impact the outcome.

2:
I want to provide an alternative point of systems thinking. The medical procedure is a process. There is a system at work to deliver that medical procedure. There are measurements to determine how the procedure is working. Efficiency (are you using the resources planned) and effectiveness (are you achieving the outcome the procedure was designed to provide) are two high-level ways to look at measuring system performance. Many measurements can be derived from these two.

From that perspective, you want to focus improvement on the areas/steps in the process that will most improve the outcome measures. With that in mind, it may have been determined that the combination of intubation materials and procedures that are used provide for the best outcomes as determined by the procedure provider. It may be to reduce cost while keeping recovery, discomfort, risk of infection, etc. at some baseline acceptable level. If you change those variables to reduce discomfort, it’s possible you may negatively impact cost, patient recover, or something else.

Note: I’m not a health care professional, so I have no knowledge about medical procedures or the various trade-offs and optimizations that take place. I am speaking from the point of view of someone who works in quality and process improvement.