A penalty box was a small enclosure where athletes participating in Human sports were often held for short intervals upon violating the rules of the game. The first use of this term occurred in the 20th century.
In 2364, Natasha Yar was sent to the penalty box by Q after refusing to take part in his "game" along with the USS Enterprise-D's senior staff. Q's "penalty box" was in fact the Enterprise bridge. (TNG: "Hide and Q")