Plot hole: Why was $100,000,000 worth of heroin sitting in the police vault all this time before the bad guys stole it? Wouldn't the DEA have taken possession of the drugs long before that?
Plot hole: Marg Helgenberger's investigation reveals that the mole has called Club Hell from the precinct. However, if you look at the scene, the villains are not expecting them (Casper spots them practically by accident and asks out loud what the cop is doing there; Noah looks incredulous), and they are even having their ether traffic in the open at the club front. Note that technically it does not say that a call was made before the blitz, but considering the mole knew about it first-hand, it's unfathomable they wouldn't tip them off. (01:23:15)
Plot hole: The movie would have been over in barely over half an hour if the detectives could access the file of Eddie Dominguez. It contained the revelation of who the mole was, which unlocks by itself access to the villain at the end of the movie. It's never explained (nor justified) in the movie why this file would be so secret and out of reach for the Bad Boys, other than to keep the plot going.
