Aesop Amnesia: In "Storm Over Ryloth", Ahsoka disobeys orders from Anakin and Admiral Yularen to pull back and gets most of her squadron killed, which naturally makes her feel upset. In "Holocron Heist", Ahsoka is in the exact same situation and given just about the same orders from Anakin and Obi-Wan during the First Battle of Felucia. The only difference is that Ahsoka is commanding clone troopers on the ground instead of starfighters. Obi-Wan tells her that Ahsoka is putting her clone troopers' lives in danger. This should have made her stop and think rather than continuing to do the same thing that she did in Ryloth, but Obi-Wan and Anakin practically have to drag her off of the battlefield instead.
Family-Unfriendly Death: In "Cargo of Doom", a Rodian Jedi Master named Bolla Ropal is tortured to death on screen by Cad Bane and the battle droids. When he finally dies, the droid operating the controls announces it in such a disturbing tone of depression in comparison to their usually high-pitched voices, you can't help but shiver.
Forgot About His Powers: In "Children of the Force", Mace Windu literally steps into a painfully obvious trap to get the holocron, despite the fact that he could have just as easily used the Force to grab it and not sprung the trap.
Knight of Cerebus: Cad Bane is one of the darkest villains featured in The Clone Wars.
Mauve Shirt: A clone trooper named Denal showed up in two episodes, and in "Cargo of Doom", Cad Bane kills Denal to fake his own death and then takes his armor.
No OSHA Compliance: Darth Sidious's secret facility on Mustafar in "Children of the Force" — besides the fact that it's on Mustafar of all planets — is built right into the side of a mountain and hanging right over lava. The computer diagram of the facility shows that the architecture isn't physically stable, and gravity supports are the only thing keeping it from breaking off the mountain and falling into the lava. That said, Sidious may have had it built that way on purpose in case he needed to quickly bury his activity, which he does when Anakin and Ahsoka trace Cad Bane's kidnappings to Mustafar, but imagine if the staff weren't droids and there was an unintentional power failure.
Smug Snake: Cad Bane is once again this. Although unlike most people that qualify for this trope, he can actually back up his smugness with skill.