It comes from a fundamentally flawed training approach. TSOs seem to be trained to function like automatons, by the book, without ever thinking about the actual mission or exercising judgment.

This approach results in the foolishness posted here; the flip side is that it also results in the constantly high failure rates during tests to see if actual weapons would get caught. It probably also ends up with a work force that sees higher attrition rates among the very people who we should want at the checkpoint - those TSOs who can exercise judgment, recognize that a clearly almost empty tube of toothpaste or a single liquid sans baggie is not the real threat.

We spend so much time programming pax about 3-1-1 and shoes in/out of the bin and ID and boarding passes ready that we inadvertently also program TSOs that these things are most of what matters.