Because if it's sensitive enough to detect a bomb it will be set off by marble, bananas or a dozen other things.

So the port only checks containers likely to have radioactive contamination, like scrap metal, which they did and they found this - system worked precisely as it should.

You could have monitors on the cranes to detect very high levels of radiation, so high you don't even want to check it manual - as in this case, But these happen so rarely it's not worth it. And with 250 Million container movements a year what sort of error rate would you need to achieve?