I feel this is mostly a prompting issue. Specifically GPT-4 shows surprising ability to abstract to some degree and work with high-level concepts, but it seems that, quite often, you need to guide it towards the right "mode" of thinking.
It's like dealing with a 4 year old kid. They may be perfectly able to do something you ask them, but will keep doing something else, until you give them specific hints, several times, in different ways.
But I've started experimenting with the second part, of sorts, not to find plot holes but to have it create character sheets for my series of novels for my own reference.
Basically have it maintain a sheet and feed it chunks of one or more chapters and asking it to output an a new sheet augmented with the new details.
With a 100K context window I might just test doing it over while novels or much larger chunks of one.
Which makes me wonder if the opposite, but more laborious approach might work - request it identify all characters and plot themes, then request summaries of each. You'd have to review the summaries for holes. Lotsa work, but still maybe quicker than re-reading everything yourself?