Plot hole: Throughout the film, Mitchell's main reason for not contacting police is that his affair and his mistress' murder would become public, derailing his wife's election and thus destroying "the one thing she built for herself". Seems odd that part of his plan is to rig his own car with explosives (from his own company), give it to the lead bad guy, then blow him and the car up on a public bridge. Certainly not a 'character mistake' as the tone of the film's ending is that, somehow, he has won, when he's failed in spectacular fashion to keep it all quiet- and his wife's been drugged, beaten, raped, and her career is over, while he's going to jail for murder.
Plot hole: If the Bird-of-Prey went to warp speed right after the whales were beamed up the ship would have already been so far away from Earth it would have been on its way back towards the sun, yet minutes later the ship is shown leaving the Earth, still at warp speed.