We have a quasilegal military prison in Guantanamo Bay. The status of the prisoners there is precarious. Military justice applies, and events are recorded and public records made.
We also have a murky gulag of international detention centers, to which various foreign terrorism suspects are flown in unmarked planes. It is not known how many prisoners there have been or what their fates have been. Nothing is publicly recorded.
At least one U.S. citizen has been detained in an irregular manner in a military prison, and his case has been well-reported and debated.
How do we know that U.S. citizens and others are not being simply picked up off the streets and disappeared? Any witnesses could be threatened into silence with the Patriot Act.
And if it isn’t already happening, how will we know? People go missing all the time. It’s a big country. They could try it out with some random people who don’t seem to matter before they went after someone who might be noticed.