This is not scientific, but I've learned to listen to subtle feelings I get when something "bugs" me. Even if I have a framework of events plotted from start to finish that makes sense, that nagging feeling often indicates where I've failed to explore conflict between the characters to their fullest. The Feeling doesn't tell me what the problem is or how to fix it, but it tells me where I have a problem, without fail. (Having people to bounce ideas with helps immensely.)
Sometimes fixing one bad feeling fixes all the other issues I had with questionable scenes like dominoes. So they could be related, if you have a few of these spots.
Another flag that something is wrong is if a solution to a problem requires too many steps to solve and becomes needlessly complicated. E.g., today I was wondering how A knows when B leaves a city, because B has to chase A, but A and B were in different cities. Instead of torturing myself with really complicated explanations involving espionage and magic, the answer was actually to put A and B in the same city at the same time (which eventually amounted to: duh!
). When issues become absurdly complicated, it means I failed to notice threads that needed to connect somewhere before the problem cropped up.
Tune in to your iffy and unimpressed feelings. That is my Magical Psychic Intuitive Dowsing Rod for Plotholes.
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