The details were not part of the reporting and it seems like many HN readers were not aware of the details until the links to the court document were posted.
What happened to him is clearly not acceptable, but the story is not "Learning Arabic got me arrested" but "handing a list of words including 'bomb' and 'terrorist' to a security screener got me arrested".
I'm not sure the Arabic is relevant - I suspect the NSA screener could not read the Arabic and could only read the English portion of the flashcards, and that he would have had similar results if the cards were in English and French.
They screen Arabs every day. They screen people who speak Arabic every day. Why haven't we heard about the illegal arrest of any of those people? Because those people don't use the English words "bomb" or "terrorist" or "murder" in front of security screeners.
I'm sure you'll find many other examples. They mostly don't get arrested, but they certainly suffer unjustifiable abuse. And keep in mind that the TSA can't arrest people, only hand them over to the local police.