Plot hole: After Margaret kills Mike at the end, she leaves through the door that is right next to his corpse, leaving her fingerprints on it, since she is not wearing any gloves. Under these circumstances, the police surely would have done some forensic investigation and dusted the doorknob for prints, which would lead back to her. Considering Margaret moved up from being a psychiatrist to a lively con criminal, you'd think it would occur to her to clean up a little bit, but she gets a happy ending.
Suggested correction: As she tells Mike, she's out of control. I don't think she planned to kill him, but he goads her into it by telling her she really hadn't learned anything and he played her. THAT was the point she learned the lesson. She took the risk and killed him. The doorknob fingerprints were a risk, but not much of one since a lot of people probably used that door before the police got there.
As for many people using the door after the murder, probably only one person might have used it if they opened it from the hallway side, only touching the hall side knob. That person would have immediately seen the body and called the police. Anyone on the baggage handling side wouldn't have touched the doorknob. Still, Margaret is not in much peril from fingerprints, since we are led to believe she has always been a "good person" who would probably never have had her fingerprints taken.
Plot hole: After Blaine gets killed and the group hose down the forest, Poncho goes and checks for the enemy. He comes back and says he didn't find tracks or blood "We hit NOTHINGGG." Now, while he would be looking for red blood, he certainly should have noticed at least the glowing Predator blood (made from glow stick fluid - widely used by the military and public alike at the time) easily visible on the large leaf, and deduced that came from something - perhaps the enemy soldier had a glow stick.
Suggested correction: This isn't a plot hole. The plot of the movie isn't broken because of this. It's an assumption that he "should have noticed" the predator blood but he might not have. And if he had, and had discounted it, it would only be a character error not to have mentioned it.
A plot hole doesn't strictly need to "break" the plot to count as a plot hole. The term most often refers to instances when a film contradicts its own sense of internal logic. For example, something happening that contradicts something else that was already established, vital information being left out, or a character acting way out of character for the benefit of the plot. In this case, this absolutely could count as a plot hole.
Plot hole: After the car burns, and they arrive at the motel, Neal only has $17.00 on him and nothing but melted credit cards, forcing him to give up his watch to help pay for the room. Del only has $2.00 but his watch doesn't quite flip the bill. At this point, between Neal and Del, they only have $2.00. However, when Neal invites Del into the room, so he doesn't freeze to death, they are eating Doritos and drinking shooters. Even in 1987 Doritos and a bunch of shooters must have cost more than $2.00. This is assuming Del didn't already have them in his trunk. But even if he did, at the end, Neal gets on his train, makes a return trip to find Del just where he thought he'd be, and then they'd both have to get back onto that train. After all, they both showed up at Neal's home. Once again, It would take money to get on that train. Four train fares with only $2.00. Neal's first trip, return trip, and Neal with Del for the last trip = four fares.
Plot hole: Senator Bunsen is introduced in the film as the President's Chief of Staff. As such, he would no longer be a sitting senator, and although he might be addressed as such, the newspaper lamenting his death would display his current title, not "Senator".
Plot hole: Eagle catches and flies off with one of the cubs and Benji goes chasing after the eagle. After a bit of searching he spots what appears to be the missing cub but then Benji is chased by the nearby eagle before turning around to drive it off. But strangely Benji abandons looking for the fourth cub, as from this point forward we only see three cubs with him. This doesn't jive, as Benji has up to this point done everything to protect the cubs and keep all four of them together. (00:58:20 - 01:00:06)
Plot hole: In the morning at the motel, the vampires have a big shoot-out with local law enforcement, which results in one at least one cop being killed. But when they escape, the police don't bother pursuing them or even giving them a another thought. Even for an 80's film, this is beyond ludicrous.
Plot hole: The fact that Buddy placed the knife and note in the steering wheel of Jerry's car is unrealistic. Buddy first met Jerry in the bathroom after school started and Jerry hasn't gone outside of the school building to his car until this point later in the morning... so there's no way that Buddy could have known which car was Jerry's to pull this stunt.
Plot hole: The police are on the trail of a known psychotic and mass murderer. When they turn up at the house of the mother superior, it's evident Ricky has been there, as the door has been cut open and kicked in. There is no way the other nun would have been able to freely enter the house without police escort, or even get out of the police car, as Ricky had not been located and apprehended. The house is a potential crime scene and she would not have been allowed in.