That’s called “foreshadowing.”
The thing is, you do notice those clues while you’re reading, they just don’t mean anything to you until later. Foreshadowing means walking a very fine line between dropping too many hints (the reader figures things out before the characters) and too few (when whatever happens, happens, it seems to come sailing out of left field, and doesn’t appear to grow organically out of the story.) Using foreshadowing well is complicated and takes a long time to get right; mostly you need practice, but:
- Look at books that you think use foreshadowing extremely well. Study those books, make notes on them, break down how they do what they do, how clues are buried in the narrative in ways that the reader skims over at the time, but mean everything later. (In Harry Potter, the fact that Lupin turns out to be a werewolf is foreshadowed by the fact that his greatest fear is shown to be of “a glowing white globe” — the moon.)
- A lot of writers use sets of notecards or graph paper to plot out their narrative. Identify the key points in the narrative (moments when characters meet each other for the first time, for instance, or when someone first notices something strange, or exhibits an unusual power (It’s foreshadowed that Percy Jackson is the son of Poseidon when several times he seems to have unusual power over water.)
- Don’t forget dialogue. It’s one of the best ways to foreshadow. A casually dropped comment by a character, a mention of an anecdote that seems related to something else, all those can be used to foreshadow and drop clues.
- You don’t need to shove all the foreshadowing and clues into your first draft, before even you know exactly what’s going to happen. You can go back and plant clues later.
- Usually, where foreshadowing is concerned, less is more.