To add to the above, small plot holes usually aren't evident in my outlines but become evident as the story shapes up. Example: one of my protagonists doesn't--but should--enlist help from a powerful but very minor character (they have a close working relationship). This minor character wasn't on my radar as part of the main character's 'resources' when I first outlined. I saw the plot hole on this latest revision.
This and a few other holes and speed bumps will be addressed in draft 6.
As a second item, some necessary scenes don't have enough heft. They were in the original outline, it makes sense that these scenes are there (from a plot perspective), but they're weak. So, revisions happen, to bolster them in one way or another. This involves adding (or deleting) stuff, which nudges the story away from the outline.
And yes, to your questions, sometimes things get ripped out altogether. Or ripped entirely apart. The query for this project was written first, over a year ago, in an effort to have a hook-y skeleton to build from, and but my project ended up looking nothing like that query pitch. Whether this is a 'better' story or not would be a matter of opinion, I suppose.
Last thing, anecdotal: One of my neighbors was a writer for Nickelodeon and we went to a taping of one of their shows, years ago. It was remarkable to see the taping of the episode, and to see this group of three writers off to the side, working in real time to adjust the lines and beats for the different takes of the scenes.