I don't know how the US process works, but long ago when I worked in a foreign country, I was required to leave the country and get my work visa added to my passport upon reentry. Reading that article made me consider that she might have been in a similar situation, only she was incarcerated for two weeks in subhuman conditions due to (at most) a clerical error.
It's really a risk for people who are not US citizens to cross our borders right now.