I'll more often find myself struggling with a story once i get to the 3/4 stage because its then that everything should be coming together - and if you've written it well enough then it will but if not... the good thing about there being a struggle though is that at least you are addressing the struggle and trying to get it right. I have to admit my inclination in those circumstances would be to just go with it unless it was glaringly horrible or problematic but then that's probably meaning my stories often come out weaker than they should :)