“’[Jordan]’s a nice girl,’ said Tom after a moment. ‘[Her family] oughtn’t to let her run around the country this way.” Tom’s criticism of Jordan is ironic because…
As Tom says that Jordan is "running around the country", he's implying she may be doing something immoral or unethical, which contradicts his earlier thought that Jordan is a "nice girl", giving a sense of irony to the author's audience.
