I've never felt comfortable with Prof Reason's "swiss cheese safety" description. It implies that environments such as aviation and medical care are naturally benign, with multiple protections in place, all functioning to optimum. Sounds nice on paper.
You're looking at it wrong. The Swiss cheese is in slices. Each slice has holes in it, which reflects the understanding that the process or check that it represents will not catch everything. However, with enough good slices, there won't be a hole through the whole stack and something will catch all the errors. Sometimes, as with this one, there may be extra holes in some of the layers, such as "airfield landing aids not functioning" and you've got a failure path all the way through because it's lined up with "pilot didn't notice X" or "Instrument gave incorrect reading" or similar. Sometimes it's as far back as "pilots were trained to do something which turns out to be wrong" (AA 191) and the fix is to teach them not to do that any more.