When does the advice "just write" not work?

I've been told this for several years now, since I got into writing. I've been following it with my latest project, and I'm nearing 100k words.

However I think I followed the advice too closely. I have an issue, I think of what to do, and I remember the advice of "just write, figure it out later in editing. It's just the first draft." I feel like it's kind of ruined the structure of my book a little.

Anyway just wanted to ask if "just write" is really a good solution to having issues with a book. Can things really be solved in editing if the bones aren't alright because I was manically typing for hours straight?