Tobias discovers that Elfangor is his biological father in this episode. In the books, this was found out in #23, The Pretender.
When Tobias sees the boy spray-painting the hawk, he only finishes the main hawk image and not the small images on the outside. Tobias makes an imprint of this main image. When he scans it into the computer however, the smaller images are present on the physical imprint, but the disappear again when the image is presented on the screen.
Rachel's Yeerk morph comes from #29, The Sickness, even though the plot of that book and this episode are entirely unrelated.
Also, in The Sickness, it was Cassie, not Rachel, who morphed a Yeerk.
Jake morphed into Tom, perfectly imitating his clothes. I might not have done well in High School science class - but I don't think clothes are included with human DNA.
In response to the previous note on a goof, Marco could not morph into the security guard because he usually had trouble morphing into morphs he had not practiced (see "My Name is Jake, Part 2" to see him only partially morph into a rat.
Goof: Tom realizes that the Andalite (Jake) is in human form, However when Jake acquired Tom's DNA to morph into him he must have felt something, and when the lights come on Tom finds himself standing next to ... himself (because Jake acquired and morphed into Tom). At this point Tom would realized that his prisoner is not an Andalite, but a human with the morphing powers, since the possessor of the morphing power needs to be in his original form first in order to transform into another creature.
Goof: Jake morphed into Tom, but when Marco attempted to morph into a security guard in the episode On the Run he failed, seeming to indicate that a human animorph can't morph into another human.
The security password of 335 (Tom's yeerk) is 1521.
We learn that the yeerk that controls Tom has the number 335, but the lettered name isn't mentioned by Inis226 (Mr. Chapman).
By book number #41, The Familiar, the Yeerk that controlled Jake in the alternate reality is Essak 241275. In this episode he's promoted to Visser Ten.
In Tobias' memory of Elfangor, Tobias asked Elfangor how he knew his name. This didn't happen originally.
How was Ax able to stand on one leg when he can't even walk on two?
Ax knew the word "wobbly" but he didn't know the word "throw" in The Escape?
What did Jake and Marco do with the Blade Ship? Did they just leave it in the swamp?
Why was everyone panicking about which button Jake and Marco hit? If they hit the wrong one, the could just hit the right one before they got too close to the planet.
The Blade ship started descending when Marco pressed a button. That is not possible in space. There is no gravitational pull so the only thing that could happen is that the ship stops where it is.
While Jake and Marco were figuring out how to start the Blade ship, why didn't the Controllers just board the ship and take them?
It's doubtful that the Kandrona would overheat in seconds. If that were possible, the Yeerks would have put in a lot more cooling equipment.
Why wouldn't Visser Three have the morphing detectors installed on the ship? He knew that he was bringing the "Andalites" onto the ship and that they had small morphs. Wouldn't he take precautions?
For just the 2 Vissers and the 2 Animorphs in the room, Jake and Marco are talking to each other rather loudly considering how quiet and prone to echoes the room is.