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: After everyone flees the family home, as Optimus is escaping he is pursued by a helicopter. He is driving down a road in a straight line. He never deviates. Yet the helicopter misses him every time, only narrowly hitting him on the side.
Plot hole: At one point it is mentioned that they have tried everything to escape the maze, and that it is impossible to climb up because the ivy doesn't grow all the way to the top of the wall. Yet in the aerial shots the ivy is shown reaching the top of the walls.