Beware of spoilers.

* The other Secret Scientist in Season 2. The kid's done nothing but ''good'' with his powers up till this point and yet at one point they are willing to '''kill''' him instead of giving him a chance. WTF!?
** Simple answer actually. 1) BadPowersBadPeople and 2) People can be [[TooDumbToLive horrifically stupid sometimes]].
** Even that one time they weren't trying to kill him. Beeman merely intended to use the Lute song to incapacitate Zak and Argost. He was going to turn it off before it became lethal. He just set his estimate for how much they could take higher than Dr. Grey did. For all we know he was right, but he was the only one of the two of them willing to risk it.
** They never wanted to kill him, but the fact that he ''could'' destroy civilization would mean that his life would be weighed against the numerous resulting casualties in a do or die situation.
** A better question would be how they found out Zak was Kur to begin with? In the season two premier, right after Doc says they need to keep it a secret, we get a TimeSkip of several months (I think, I don't remember the exact length given), and suddenly the Saturdays are fugitives from their friends (and possibly official authorities) and Argost is M.I.A, presumed K.I.A. What the hell happened during that time?
* In "Guess Who's Going to Be Dinner?", Zak and Fiskerton break into the "Experimental Weapons" vault. When the Big Bad of the episode is chasing them, the handful of weapons Zak grabbed prove to be useless...except for when they spill out of his hands, and it was revealed that his mom's fire sword was among them! First, why was one of the family's MAIN WEAPONS/one of the most valued possessions Drew had in with the useless junk in the Experimental Weapons vault? Couldn't it have been put somewhere more secure? And that sword is at least three feet long; how did Zak not notice he had it with him along with the other weapons? The way he says "Mom's fire sword" sounds like he was surprised (albeit relieved) to see it.
* The subplot with Doyle and the ancient Kur-sensing relic is just a whole mess, really. It is shown that it can activate at long distances, because it does so when Doyle's flying over them all in a plane during ''Kur Rising'' and he's several hundred feet from everyone else at the time. Therefore, it should have glowed many times during ''Shadows of Lemuria'', because it was constantly in the same house with Zak and even in the same room when he walks in on Doyle fixing it. While the twist it led up to was interesting, many of the things they forced in to set it up don't really work well when inspected closer.
** Speaking of things used just to build up the twist, the whole thing with Antarctica. Seriously, why did the dousing even send them there if Kur was with them everywhere, all the time? There was nothing in the show to connect Kur with Antarctica, before or after, since the giant Cryptid they found was literally just a random giant Cryptid.
*** The WMG page has the Antarctica Cryptid as a part of a Self-Sustaining Death Trap for anyone trying to find Kur. It was never actually stated that they would find Kur there, only that they needed to go there.
*** Fisk didn't actually claim that Kur was in Antarctica. He prophesied that Kur would be revealed at that location. Call it a self-fulfilling prophesy of sorts. Also, the Kur-sensing relic probably didn't work until it was repaired.
*** But Doyle ''did'' succeed in repairing it--still inside the same house as Zak. Why didn't it go off when it was fixed? Surely if the Kur-sensing relic went nuts as soon as it was fixed, Doyle wouldn't have kept that quiet.