Many bad guys that should not be able to be there (Malchior should be trapped in a book, etc) are present with no explanation.
Just before the final battle, the camera pulls back to show the array of bad guys. Hotspot is shown on the far right. He's a honorary Titan, not a bad guy, and should be frozen at that moment.
After the final battle, just before and after Beast Boy and Mas y Menos freeze The Brain, there are views of all the gathered teen heroes. Just before, Puppet King is shown with the heroes (far right), and just after, an arrow-headed villain is amongst the heroes. At this point in the plot, all the villains had been frozen, and wouldn't be standing with the heroes.