Plot hole: If Old Biff changed his past and went back to 2015, he goes back to HIS future, not the bad future, but Doc later tells Marty that if he were to go to the future to stop Biff from taking the almanac, he'd go to the bad future, so Old Biff technically shouldn't have been able to return to "his" future at all.
Plot hole: When the ship has turned on its side for the brief moment, it cuts to inside the ship where a hallway explodes, causing the ship to submerge. The only problem is the people are standing on the ceiling, but if the ship's on its side, they'd be on the wall, not ceiling.
Plot hole: Radl and Steiner discuss the entire scheme to kidnap Churchill on the Alderney docks - in full view and hearing of a number of civilians (who shouldn't be there, pace another posting), including local fishermen. Though the Germans banned all fishing activities in the Channel islands including Alderney in 1941, they were well aware that there was a flow of information from the island to military authorities in the mainland. Why would they be so stupid as to discuss a top secret military mission in public? In reality, they wouldn't even discuss it in front of their own men.
Plot hole: During the end the murderer is thrown out the front window of the building. The students leave the building through the front door, but yet there is no body, and that doesn't seem to bother them!
Plot hole: In the final tournament when Happy is stuck in the rough, he swings five times. Assuming he hit his drive into the rough and hit an AMAZING shot from the edge of the water into the hole, he still could do no better than a seven on the hole. Happy only lost one stroke on the hole. (01:16:50)
Plot hole: The Toymaker throws that toy bird at the hippie version of himself. The toy goes through him because he is a hologram. Later, he pushes the soldier version of himself at the screen making it crack. How could he if the three others are holograms?
Plot hole: A detective would never be assigned to a suicide scene, since suicide is not a crime. A detective would only be assigned if the suicide is actually found as a murder. Nor would a detective be assigned to find out about a potential sexual relationship or affair unless it involves a crime.
Plot hole: Barry gets killed violently at the pageant. So obviously there should be blood everywhere. When the police go up to the crime scene, they find nothing. There's no way the killer had time to clean up anything, let alone drag away Barry's body without someone seeing him. And blood starts dripping after the police leave the scene.
Plot hole: When Jake first meets Reggie, he tells Reggie that the Great Turkey told him everything about him. Later in the movie, when Reggie goes back in time and introduces himself as the Great Turkey to a young Jake, he only tells Jake to find the "Pardoned Turkey" but never said that the pardoned turkey's name was Reggie, so there's no way the adult Jake would know Reggie's name when they first meet.
Plot hole: At the beginning of the movie, Hedwig rattles her cage, and Harry says apologetically, "I can't let you out, Hedwig; I'm not allowed to use magic outside of school." But he wouldn't have to use magic to let her out - the key is visible sticking out of the lock on the cage, so all he would have to do is turn the key. (00:01:10)
Plot hole: When Moana first meets Muai, she opens her necklace to tell him he will restore the heart. Muai sees the heart but doesn't get scared until he sees it again on the boat. He should have been scared the first time.
Plot hole: Swapping his dental X-ray records with his deceased partner won't convince anyone that Varrick is dead - then (as now) the patient's name appears on the X-ray.
Plot hole: The T-X did not hear Catherine in the Animal Hospital when she was only a few feet away and breathing loudly. Considering the scope of some of her technology, one would assume she would easily find her. (00:22:20)
Suggested correction: This isn't a plot hole. It's just your unfounded assumption. There's no evidence to support the supposition that the T-X has such audio detection capability.
Even if she could detect it, how could she discriminate between the sound of Catherine breathing and that of the dozens of caged animals in the room? That's stretching even fictional technology a little far.
Plot hole: In the air vent, we see a rat. Wouldn't rats in the vents set off the alarms on a regular basis, because the lasers were on the upper side of the vent?
Plot hole: SPOILER: When Amy comes back, doctors would have checked her non-existent head wound from the "abduction", from where she supposedly lost that much blood. That would and should have revealed all of Amy's lies.
Plot hole: When Vers arrives at the bar, Nick Fury is already there. She went straight to the bar after stealing the bike, while Fury needed still to learn about the theft, link it to the case, with investigations taking place to maybe (only possibility that would not depend on the vehicle being reported) figure out that Pancho's was the destination from examining the search history of the browser. Fury went there by car. His boss also explicitly says to work on the case alone. Amazing he could be there with such timing.
Suggested correction: Vers probably got lost and had to wander around to find the place.
I can't realistically say it's impossible (it is not shown, after all), but nothing in the movie implies it, and it's the exact opposite. She is shown, driving, fast, on the Sierra Highway, which is where the bar is. Not stopping to ask for directions or at crossroads (something it takes 1 second of movie to show). In perfect Star Trek tradition she can speak the language, she reads the maps just fine, in fact she already looked the place up on the map, that was next to her and she already knew how to use without help, before taking off on her fast bike not hindered by traffic. And again, the head start she has is huge since Fury can begin investigating only once he hears about the stolen bike. Fury is at his HQ and a long time seems to have passed, since he is patched up and a whole autopsy has been done. Vers started searching right away.
Suggested correction: The effects of the past being altered may not have happened immediately. It is possible that it took time for the timelines to adjust to the changes of events, meaning enough time would have passed to change 1985 when they return, but not enough time could have passed to change 2015. By the time Doc says if they went back to 2015 they would be going to an alternate future, some time has passed, so the effects of the past being altered and taking ahold in 2015 and altering it are more likely to have occurred by then.
Casual Person
Here is what you say: "perhaps it took time for the time lines to adjust." What kind of time would timelines take? Time is time, it doesn't take time to change the timeline. That doesn't make any sense. Some people claim it was the DeLorean itself that came back to its own original timeline and only then reset itself in the new one, but then the new timelines being erased later on wouldn't have happened either. So its a genuine plot hole.
lionhead
It's established in the first film that it takes time for the changes to take effect. Marty and his siblings slowly disappear from the photo, rather than instantly. Although the scene in BTTF2 was deleted, it was filmed showing Biff dying and slowly fading away after his return to his present.
Yet they were restored instantly without any outside influence at the end of the movie. There are a lot of things wrong with this movie and the first one. Old Biff disappearing should mean that Marty and Doc should slowely disappear as well, even the DeLorean. But they didn't, that doesn't make any sense. The point is there is a plot hole, somewhere. To know where all you can do is look at it logically and then you automatically come up with Old Biff going back to the future but not the alternate future. If he did there wouldn't have been a movie, but that's the plot hole.
lionhead
The timeline didn't change until he made his first bet which was some years I think after receiving it. He immediately travelled forward after giving the act, meaning he will still jump forward to the original future.
The timelines would instantly change, and Old Biff couldn't possibly have returned to "normal" 2015. It's just a poorly-thought-out time travel plot hole (or a deliberate error to expedite the storyline).
Charles Austin Miller
Suggested correction: In context, Doc was saying that they couldn't return to 2015 to stop Biff from stealing the time machine, because Biff didn't steal the time machine in the alternate 2015, he only stole it in the original 2015. Marty and Doc didn't stay long enough in 2015 after Biff returned, and that's why they didn't see any differences. Also, though they were unaware of it, Biff was dead in the alternate 2015, so the disasters he caused might have reverted back after his death.