You might as well get used to the idea.
But it's not as bad as it sounds, because in the rewrite phase, you're working just as creatively as you are in the first draft. Sometimes more so.
The fact is that stories rarely come out right the first time. Occasionally sentences do. Or paragraphs. But whole stories? Almost never. Maybe the beginning isn't right or the ending. Or the middle. Maybe the whole blasted thing isn't working, and it's because there are a lot of things wrong. Maybe you have all the pieces, but your aliens sound like humans, and your humans sound like computers. Maybe your plot doesn't make sense, because you have three major coincidences, and your ending feels contrived.
Welcome to the club. What you have to do is deal with it one step at a time. Want to see what one of my pages looked like after I was done marking it up? (This was a page from a book that had already been published, and I was revising it for a new edition. I found quite a lot to change!)