In the previous episode, Janet got a fortune cookie that read "Kill your neighbor and you'll go free." The piece of paper with the fortune on it had the fortune in one single line, but when she pulls it out in this episode, the text is in two lines, broken after the word "and".
The first time Janet Cooper looks at the paper from the fortune cookie, the message is a single line. When she looks at the message right before she tries to run, it is now two lines.
The butterfly in the jar is not a 'Vanessa cardui' as stated by Moira when she looked at the caterpillar earlier.
When the captives are sent to The Program's town in South America looking up at the stars and pointing out the Constellation Cassiopeia they should have noticed the stars were different from home, and there were constellations that they didn't normally see.