Actually, this is quite common, it’s not an anomaly. Writers start with an ending in mind, then as they write, the story takes you in a new direction. This happens all the time. A wrier needs to go where the story takes them, if you rigidly stick to your initial idea, it’s not going to be as good.
From day 1, we knew the murder was not important, it was never planned to be. Initially, there was a different ending, but the theme was the same, then as I wrote, this ending felt better and more salient, and matched the theme of what was happening better. The act of going into the wireframe world was initially an easter egg, but as I got to the end, it made more sense to require it.
The ending of MI2 came to me about 2 months before the game shipped, mostly driven by the panic of not having an ending, or more correctly, having a crappy ending I hated.
My point is, endings change as you write, because you start to understand your story better. People like to think books, movies or games are fully formed ideas that just pour out, but that’s not true. It’s all made up anyway, so why not change it as your creating.