When the torpedo scene on the boat is at night, and it suddenly switches to George and Peter on the civilian boat in the daytime, it is.
It's weird because you see the stories converge near the beginning, when the planes fly over the boat that is part of the rescue, so it seems like they are going on at the same time.
I don't know, I can understand why people would find the editing confusing. They might chalk that night time scene up to a continuity error or something.
David Bordwell just posted his Part 2 about the movie. The first entry was about the structure this one is more about the style and he goes a little in-depth about the crosscutting.
http://www.davidbordwell.net/blog/2017/08/09/dunkirk-part-2-the-art-film-as-event-movie/
The crosscutting is one of the issues I had with the movie when I saw it; I mentioned it (and forgot that Inception has the same thing, but it's more obvious).