Sometimes rules may go against some specific cases of "common sense", but they are made, so that, as a whole, revenues are maximized and operations are optimized.
When you have, say, 90% of satisfaction, it takes a heavy investment to grab the additional 1 point. At this stage, the company will weight the additional revenues that it may generate, and the cost of the service before going further.

If you are a top premium player, you can target 100% satisfaction, because your clients are ready to pay for it.

But, EK is not a luxury carrier. It's mass-market, it's growing very fast, and fares are usually cheap. Therefore, they need to have strict rules, which, in few cases, may appear stupid.
Everybody have examples of lost opportunities for "common sense".
To avoid that, you need to have staff that are trained, that have experience, that know very well the functioning, that have networks, that have imbedded sense of service, that are truly dedicated to the company. All this is indeed a cost.