Plot hole: Zharko's process of using the dead bodies of agents and reviving them could only work if he had them at about at most a day after they were killed. Since his secret lab is on a deserted island in the middle of nowhere, they could not have got the bodies to him in time. The Chief also said that the bodies suffered severe damage, so their ability to move would be seriously hindered, but they work fine.
Plot hole: The scheme to lead a blindfolded Max and 99 to what they think is the airport via an illusion room would not work the way they do it. Since the base is underground, there is no way that what they did to represent ascending to ground level that would make a person think they were above ground.
Plot hole: In this episode, the villain makes a phone call to KAOS headquarters when he's captured demanding that they kill Max to stop him testifying in court against him. Later, several say that Max is the only witness to the villain's crimes, but the Chief and 99 were in the room when the villain made the call, so they could have been witnesses to "conspiracy to commit murder."
Plot hole: Doctor Yes' execution trap involves a booth flooding with water, drowning the occupant, and the water pushes a float upwards, eliminating another via a spinning blade. However, several times the float reaches the top of the booth, and the spinning blade doesn't kill anyone. There's also a breathing space at the top of the booth, so people couldn't drown in there.