You can plan out a novel or short story as much as you want. Some people use elaborate outlines, plot character arcs and development, devise color-coded index cards to document chapters and scenes, etc. (And for the record: I don't do any of those things. I know where I'm going generally, and I'll list out things I want to happen or cover, but I tend to discover as I go, for better or for worse.)
But sometimes it happens: you reach a point in your novel or short story where you thought something was going to occur, but when you finally arrive at that point, you realize it's not the right thing for the story. What it comes down to is this: it doesn't feel right emotionally; it feels wrong.
This happened to me recently. For a long time, I thought the reunion of two characters in my novel would happen at the very end of the book. But when I came to a certain point, I knew that it had to happen sooner. Emotionally, it felt right. I fought it for a while, but I came to the conclusion that I couldn't keep these characters apart any longer. Emotionally, it was time for them to meet again.
And it's happened before: In a previous novel, I envisioned an act of violence occurring in the closing pages. But after having written the novel, it just felt wrong and out of place (it was, primarily, a satire and comedic, and violence and satire/comedy don't always mix so well; emotionally, it felt wrong).
The point being, I guess, is that you can plan all you want but ultimately you have to be true to the story you're telling and what feels true/right for your characters.