WHY YOU DUMB MORTAL, QUESTION THE ALL POWERFUL CASSIE MAGIC?
Here's a different explaination. (This is after Cassie has been "trapped" as a caterpillar.) Aftran runs off to the State police-Controllers, and says she lost track of the Andalite Bandits, but she's safe now. Aftran doesn't tell Yaheen 747 and the others what she knows, as part of Cassie's peace treaty. The next time Aftran and Karen go to the Yeerk Pool, Aftran gives her instructions. At the unloading pier, she tells the Hork-Bajir-Controller guard there that Karen is a voluntary host (now?) and has permission to go to the cafeteria (or wherever). Aftran instructs Karen to wait in the café for a few minutes, and then walk out as if she's a Controller. This is how Karen gets away free while Aftran stays in the pool as per her promise to Cassie.