I read threads about some TV shows on the TiVo Community forums, specifically Now Playing, where some shows (notoriously especially Lost) get analyzed to death. I sometimes have trouble expressing a concept when people talk about plot holes, where something that the story depends on doesn't make sense or fit with what we learned before: namely, that some matter, and some don't.
How can a plot hole not matter? The key question is this. Could you plug up the plot hole by inserting a few lines of dialogue which would resolve the issue, and change nothing else in any significant way, and not contradict anything else already established? Even more so, could you do so in such a way that the dialogue added no entertainment value, and better yet, just bogged the show down in a bit more exposition, serving no purpose but to plug the plot hole?
If you can, then the plot hole doesn't matter. Just imagine that scene with the dialogue you need got filmed, then got cut for time. If there are multiple possible explanations, just pick one, since we've already determined that any of them would change nothing else in any significant way, so it won't matter which one you choose.
For example, perhaps a bit of a story depends on the fact that a particular character hasn't had a date in years, but there's no particular reason she couldn't get a date; she's cute enough, she's wealthy, whatever. That she hasn't had a date in years is not a big turning point or an important fact, save only that it is the impetus for her to do a particular thing that turns out to be interesting or important. That she hasn't had a date is mentioned and then the story moves on from there. Some people object: how could she not have gotten a date for years?
Let's say that, based on what we know about her, it's entirely plausible that three years ago she had a bad breakup and stayed out of the dating scene for a while, maybe had trouble trusting people. Maybe she's just shy. Maybe she has particular tastes for a particular kind of partner. Maybe she's hesitant to accept any overture that she thinks is just because of her looks.
Since nothing in the story depends on why she hasn't had a date, and we can invent any number of plausible reasons which contradict nothing past or present in the story, you could insert another throwaway line or three into the story that answered the question, and then everything would work. Removing those lines doesn't change anything, it just leaves an unimportant question unanswered. But it's possible that it makes the pacing of the story a lot better. We might feel like we'd rather have everything answered, but if we did, we might complain the show is too boring and talky. Sometimes, we never find out what something is not just because it doesn't matter but because finding out would detract or distract from the story (as in the famous case of the Maltese Falcon).
By contrast, if there's no way to explain away a contradiction or seemingly implausible fact that doesn't also require you to posit something which would affect the show, or be too important to be brushed aside, have a significant impact on the character, or change things the characters would do, then the plot hole is a real one that matters. Or if there's no way to fix the plot hole in three lines of dialogue, then it matters. Either the writers will address it later (by revealing how some previously assumed truth was wrong, or adding some new element to the story), in which case finding it might be finding a clue; or it'll just sit there as something that you have to not look at too closely.
So many people get so burned by plot holes and so used to looking for them that they can't see how some of them are, or might as well be, nothing but editing choices. It makes it harder to make real plot holes as important as they should be, when they're drowned out in ones that aren't.