There's loads. I'll add to this as they come to me.
First that pops into my head is Alien.
They were heading so far out into space the crew needed to be put into suspended animation for the duration. Yet one of the crew was an android so lifelike that it passed for human. None of the crew knew he was an android until he was torn apart.
The most obvious question is: why didn't the mining company just use androids? Why bother with the cost and hassle of a human crew when androids would be more efficient, stronger, work harder, more intelligent, wouldn't be paid and presumably not need food.
Another movie, another plothole. Three, in fact.
Raiders of the Lost Ark
1. Indiana Jones swims over and climbs aboard a U-Boat which then, for no reason, putters across the Mediterranean not bothering to submerge despite the Nazis trying to hide what they're doing or carrying.
Raiders of the Lost Ark (1981) – The Nazi Submarine – A Steven Spielberg Film
Indeed, if the nazis at around the 4-minute mark of the above clip are to be believed, they did in fact submerge. You can hear them say, “Tauchen, Tauchen das Uboot!” (“Dive, dive the Uboat!) I know he's Indiana Jones but surely even he can't hold his breath for that long!
2. If Indiana hadn't snuck onto the submarine, the Nazis wouldn't have opened the Ark until safely back in Berlin. In which case this:
Would have been Hitler. Indiana Jones' hubris resulted in WWII, the Holocaust and the deaths of an estimated 80 million. He's not a hero, he's an utter c**t.
3. The Ark of the Covenant is this incredibly powerful, destructive weapon that comes from God himself and is capable of destroying everyone within range…but only if you look at it. Close your eyes and it can't kill you. Is God a toddler with whom you can play that game where you close your eyes and say, “Where's god? Where's god? There he is!”
Another couple I just thought of:
Citizen Kane
There was no one in his room when he utters, “Rosebud” and drops the snowglobe.
Citizen Kane snow globe
So how is it possible that a newsreporter is assigned to investigate and decipher his dying words?
Batman: The Dark Knight
First shot we have of The Joker is this one:
Which means he's standing in broad daylight on a busy city crossroad in full joker make-up. Okay, not a plothole but just silly.
The plothole is the bank robbery. Every man has their own specific job to do that they need to do in order with one other of the team with them, who then kills them and goes off to do their specific task with another team member who then kills him, up until we get to the Joker who is about to be killed but is saved by the bus reversing in at high speed right where Joker's would-be killer is standing.
Anyone else see the problem with this?
The Joker had to assemble a team of highly experienced bank robbers who all have specialist skills yet did not know each other. In addition, each of these men were also cold-blooded killers who were easily convinced to kill their own (being a bank robber does not necessarily mean being a murderer). On top of of this, despite being extremely skilled in bank robbery and being heartless killers and double-crossers, they were none too bright. None of them stopped to think, “wait a minute: if I am to kill that guy after he has killed that other guy, after he has killed that other guy, might it be possible that this bloke standing next to me has been told to kill me after I've completed my job?”
Despite being so well trained, they also either did not train together or, if they did, never let on to each other their secret mission to kill.
At the end of the scene, the Joker had to rely on his killer not to shoot him earlier, to be standing in the exact spot the bus hits, for the bus to bust through at that exact time, and for the bus to be able to break through the bank wall.
Statistically this fails. Joker had to assemble a crew who were: Extremely experienced, did not know each other, were not friends, could be convinced to kill each other, did not talk to each other, were happy to be hired by someone they did not know and never meet, and were not bright enough to analyse their situation. And, iirc, Gordon (or someone) says that The Joker has done this several times. Which means he has repeatedly assembled a team of experienced killer bank robbers whom he then wipes out each time he robs a bank. You would think after the 2nd or 3rd time this happened, the bank robbers in Gotham would baulk at the next anonymous phone call requesting their services to rob and kill.
There were so many holes in the bank robbery scene it became farcical. It was obviously written in order to make us all think how 'awesomecool' The Joker is. Which is not good storytelling or filmmaking.