As you are writing, do you hit a part of the story where you need to do some research?  For me, since I'm currently writing science fiction, that occurs often.  As I write, I stumble upon something that makes me go "hmm, is that true?" and then I go off on a tangent, searching reddit and physics books to see if that really is true.  For example, my latest bug is whether or not the crew would feel forces as they did a flyby of a planet.  My instinct is to say no, they wouldn't feel a thing.  Then again, I don't have a doctorate in astrophysics, so what do I know.  It's important to my story, because I'm having the captain force the ships to separate so they can do the maneuver.  It might change my story if they don't need to separate.  I want them to separate so that bad stuff can happen to one of the ships.  So, this pulls me out of my writing, and I go on a long journey of finding out about astrophysics.
If I don't pull out, I could wind up writing a plot thread that isn't possible.  This is the problem with hard physics.  But, I'm assuming this same problem occurs with everyone.  If you are writing a mystery that takes place in another city, you probably have to research that city a bit before writing your story.  However, once in the heat of battle, when you are elbow deep in your scene, you hit some area where you just don't know, and it very well may affect your entire scene.  
What do you do?  Write on?  Stop and research, hoping you don't lose the moment?  Ugh!
Popular wisdom says to just write and don't edit while writing.  You can't control what goes on the page, but you can damn sure control what stays on the page. 
I've found this as the best advice.  So, whenever you see a boulder in the road, just write around it and keep going.  You can always come back to it after you do some research.  If you just can't find the answer, maybe it's time to just re-write the entire scene.

That moment when you send your story to a beta reader, and you realize there is a major plot point you changed in the front of the book, but not the rest of it!  Ahh!
As I'm going through the book on my own, I realized I sent it to two people where major plot points have changed.  I should have taken the time to go over it one more time before sending it out.  But, then again, there are many other issues with it, I'm sure.  I don't get the impression that books are ever "done", you just get them to a point where they are publishable and they go out.  I'm sure Lee Child could look back on a novel and change something about it.  I mean, the same thing happens to musicians after they put out music.  During the live performance, they add in new elements.  The basic structure is there, but minor elements change.
So, why should I worry?  I'm sure they'll get it.  Well, as a precaution, I sent them each a message indicating the major plot point changes.  It's still out for beta, so we'll see what comes back.  
Anyway, continuing on this re-write.  If anyone has any suggestions on when to send to beta readers, or when done is done, I'm all ears.