Sometimes in a book a character will do something odd or confusing or wholly out of character, but it will be explained later and make perfect sense. The problem for the reader is that they don't know whether the ‘mistake’ is intentional or not. This can sit in the reader's mind distracting them, or even annoy them so much they give up reading the story.
With an established writer most readers will just take it for granted that it will probably turn out okay. It may not, but most readers will give the author the benefit of the doubt. But with a new writer, especially if it's an agency or a publisher that is reading it, so often does it turn out to be an actual mistake, the character just behaving inconsistently, that it is safer to assume that the writer just doesn't know what they’re doing.
So, for example, maybe a character drives a car with great skill at one point and then later drives in an inept manner without explanation, and the reason turns out to be that they are a spy undercover and they know they're being watched so they have to you act like someone who isn't a spy — because these things are all spaced out over possibly many hundreds of pages it only becomes apparent what's going on after you've read the whole thing. It would be nice if the person reading just trusted the writer and hoped for the best. Unfortunately they will have been disappointed by that strategy so often that the likelihood of them doing that is pretty much zero.
But it may be a key part of the plot and something you don't want to radically change or make too obvious. Fortunately there is a very simple solution.
Have a character within the story notice that something doesn't make sense or seems odd. Even if it's just in passing, a casual comment that goes no further, that doesn't reveal anything and offers no answers, that will be enough to clue the reader into the fact that you have things in hand. If you know it doesn't appear to make sense and you let the reader know you know it doesn't make sense, then the reader will trust you have your reasons and that you will explain yourself eventually.
How you go about this and how subtly you do it is down to individual preferences and the specifics of the context.
But if someone tells you they don't understand what's happening or why it's happening or that it seems contradictory, and your thought is 'That's how it's meant to be!' and they’re being too hasty in making a judgement and should just read on to find out, try to take into account that an agent or publisher (or much more likely one of their readers) will probably have a similar response and be even less likely to keep reading.