The trickiest place in writing a novel is the middle of the first act. There is a lot to do. One of the hardest critiques to try and fix is a chapter in the first act where you've dropped a huge clue and the critiquer says, “Well, that was fun and showed something about the characters, but how did it move the story along?”
It makes me feel like a stripper who is preforming in a low class club. I'm trying to do flashes and teases while the audience wants immediate gratification.
There is a fine line between putting in the plot point so subtly that the reader says, “I didn't need to know that little detail so I'll skip it” and writing “PLOT POINT:” just before a paragraph.
Another problem with leaving subtle clues is trying to fool your main character without fooling the reader. In one novel I have a character who breaks character often. In the first draft I just had her do that so once the reader found out why she was doing it they would go, “So that explains that.”
In my first read through I could see that a reader would think one of two things. I was a horrible writer who couldn't keep my character in character. Or, my main character was really dumb. I wasn't going for either one of those so I had to rewrite those parts so my main character notices the changes but has a reason to ignore them.
One tool I use to help me with my plot points is a spreadsheet.
I started this just to keep track of my progress. I'd put the Chapter Number, Chapter Name and word count in a spreadsheet and have it add up my word count so I could see where I was in the book.
I changed that later to help in editing by adding a description of the chapter. This not only helped in editing as I could quickly find a chapter but I could also see how the novel progressed. So I put another column in labeled “PLOT POINT”. Every chapter in my books have at least one.
When I go back through, I see if the plot point is obvious or buried. Then I can work on it. It works pretty well for most of the plot points and points out the problems, fixing them is a little harder.
My worst one so far is it is important that for the reader to see that Howie, a college freshman, knows what a bandelore is. He has to think it is natural for him to know about bandelores, Packard twin-sixes, and other things from the turn of the century, but so far my beta readers are missing that plot point and laughing at my dialog. So even being able to pinpoint where the problem is doesn't always lead to a solution.