Continuity mistake: Max and 99 are sitting on the sofa. There is a knock at the door and Max fires 3 bullets into the door from a gun. Later, the same day the door is shown behind Max and 99 and there no gunshot holes in the door. Also, 99 changed her clothes and Max still has on the same clothes. (00:09:00 - 00:19:00)
Visible crew/equipment: When Max and 99 are trapped in the room with the hatch that leads down to the Guru's chamber, the filmmakers didn't bother to make it seem like a giant hole in the ground, and they also didn't bother about the floor of the set being about ten centimetres below the hatch.
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.
Factual error: If there really was a hatch leading into mid-air in the airplane bathroom, instead of being soundless like shown, it would be incredibly loud and Max would have noticed. Also, the sudden pressure change would have sucked him out no matter what he did to stop it.
Character mistake: The leader of the Purple Knights says that they would only be bike riders if they couldn't tell which gender someone was by their hair. This is a major mistake, because if you look at the hair of the Purple Knights, it's incredibly easy to tell which gender someone is.
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.