Plot hole: In the scene where bad cop says "security cameras picked up this" it shows the footage of Emmet "convulsing with the strange piece." If they had cameras down there, then they would've already found the piece of resistance. (00:08:10 - 00:10:10)
Plot hole: Once Time Trapper has been stopped by Dawnstar and the time vortex in the sky stops sucking things up, everything in the air just hovers unmoving completely. Except for the people. Somehow Batman and Robin and Superman are able to move around just fine in the same time and gravity frozen place, Robin even jumps from hovering rock to rock without them moving. In fact, as soon as the sucking stops, the tree that Karate Kid is hanging onto stops moving and does not fall, but gravity somehow instantly affects Karate Kid and he almost falls off the tree and has to catch on again. It makes no sense at all for the objects to be affected and stand still and the heroes to not be.
Plot hole: The main plot of the film involves Iris and Olson's mission: Destroying the Mobile Fortress 000. But Iris is a special gynoid. Her primary function is to activate the Mobile Fortress. The antagonist of this film could unleash calamity if he had Iris and the fortress. So, which idiot has sent Iris on this mission? The logical course was to send a demolition team, or better yet, send no-one at all. Anything is better than sending the activation key outside the safety of the Olympus.