Well, I mean when you think about it, a group of "Andalite Bandits" theoretically shouldn't have been able to seize the ship anyway. If the kids were a small band of Andalite warriors working on their own, without the help of the Chee and all their other allies like Eva and Toby, the Yeerks would be right - the Pool Ship couldn't have been seized.
So the precautions they took with the changing of the access codes, and the multitude of Bug Fighters flying patrol, and the buttload of Hork-Bajir in trigger-happy mode, and the giant area of scorched earth they'd created around the landing zone, that all seems pretty reasonable and sufficient.
I agree with you that the Yeerks were portrayed as more than a little incompetent throughout the series, but the fact they landed the Pool Ship and didn't expect to be taken over isn't really a great example. It's probably one of the only times in the books they ever did act with reasonable initiative and concern.
But I totally agree about the "big red button that happens to flush the entire pool into cold dead space" point. That's just a limited point in that plot though.