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Later in the article it points out that an undercover person would arrive on a passport under a name but then check into a hotel under a different name. In that case it would trigger the alert that the passport name never arrived at a hotel. It also says that the practice had to change so that an undercover person used only a single persona for a country instead of having multiple personas and switching between them.

My thoughts exactly. Don’t agents try and blend in by keeping a unremarkable profile? Once you’ve arrived your schedule can be anything you want.

I'm sure they did, but that is just one example.