Those nasty things. They are rather like potholes -- irritating things that won't necessarily prevent you from getting where you want to go, but they annoy the hell out of you and seriously impede your ability to enjoy the story.
Small potholes are fine; often you don't even notice them.
The big ones, however, are awful.
In fiction terms, you're allowed only one major plot hole per novel, if you even have one.
Smaller ones are often ignored or undetected.
And the more fancy and out of this world your story is, the more your readers would suspend their disbelief and accept more plot holes. But even they have limits. Men who could get pregnant and deliver babies may work in science fiction, but you still have to explain that enough to make it plausible. Then you'd need to add all the complications (for example, men are not going to be able to give birth naturally, no matter what science says).
Take a classic movie, Raiders of the Lost Ark, for example. I love that movie, and it's a rollicking good time. Much of it makes sense, in the context of its fantasy. After all, we're talking about the Ark of the Covenant and the power of God. Still, if you must, you have find plenty of plot holes or illogicalities:
- Indiana Jones is a professor, but it doesn't seem like he teaches much. He was shown to teach one class, but then suddenly he's on a globe-trotting trip to find the ark
- Why does everyone call him Indy if his real name is Henry Jones Jr.? At least his employer would call him by his real name
- Indy hasn't seen Marion for over 10 years and she's hiding in the Himalayas and lo' and behold, he finds her
- They are pushed into a pit down 30 or 40 feet... neither hurt themselves; not even a sprained ankle
- And so many snakes in that pit... what do they eat? I'm sure not every day there is a person being dropped into that pit... are they cannibals? And where did all those skeleton come from?
- Oh right, Indy swims to the submarine (undetected) which is about to go under... and he survives the trip all the way to the island!
- The car chases are great, but let's face it, they are un-effing-believable
And that's just some of the plot holes and inconsistencies. Wait until you see The Temple of Doom.
But, do they matter?
Not to me. That's the thing. The characters and the story are so engaging that I hardly noticed the plot holes. And when I did, I didn't really care, because the movie was so well done.
I remember a friend of mine read the shooting script of Raiders of the Lost Ark, and he thought it was crap. The worst thing he ever read. And I could imagine why. It probably did sound cheesy on paper, like one of those bad B-movies. But when he saw the movie, he was blown away and thought it was one of the best movies ever.
You can have the best idea in the world, and if your execution isn't up to par, it'd fall apart.
You can have the worst idea in the world, but if your execution is Spielberg-esque, you may be able to make gold out of dirt.
What Raiders of the Lost Ark illustrates is that given a preposterous story and larger-than-life cliches, it could work, and work beautifully. Everything worked in execution, from the perfect casting (can you even think of anyone else playing Indiana Jones? Didn't Indy and Marion have great chemistry together?) to the location shots and action scenes, and of course the bone-chilling finale. Everything works together, even if the script sounds cheesy and outrageous.
Oh, right, and there is not ONE major plot hole. All the holes I mentioned were minor. Over all, the plot makes sense. Going from point A to point B makes sense.
Spielberg passed the "one major plot hole per story" test.