I watched this movie 3 times. Each episode did not END with all at the same time. The ONLY part that all happened all at once was when Farrier shot down the bomber which started the oil fire, at that same time Peter was able to pull Tommy onto the boat, while the civilian boats were loading up the remaining soldiers at Dunkirk.
The timelines are like this as shown in this diagram:
You see the story about the soldiers from the mole started BEFORE everything else did. All the events that happened leading up to Dawson's ship finding Cillian Murphy on the wrecked destroyer happened before Dawson's ship left. The day Tommy and Alex were rescued was the 6th day. Had it been ALL on the 7th day, the non-linear storytelling would of ENDED the moment Tommy and Alex were rescued and everything would of been linear from that point. But it wasn't. After Dawson and his people rescued Alex and Tommy and the rest from that one ship, they encountered another German fighter jet which was the same fighter jet that Farrier shot down saving those at Dunkirk right before he landed while out of fuel. So, all of their stories did NOT end at the 7th day. Farrier's was the 1st to end which was when he was captured by the Germans. Dawson and Peter's story ended that next morning when Peter went to the newspaper to submit George's picture, and Tommy's and Alex's story ended much later on the train reading that newspaper.
Nolan DID NOT stipulate that the timelines were solely the length of them being on the beach... it was the length of each TALE. If it wasn't, none of those stories wouldn't of intersected to begin with. But everything is connected into one big story. So, in order to understand how Cillian Murphy GOT back to the wrecked destroyer, you HAVE to take into account everything leading up to BEFORE the Dawson's story even began. And one way or another, Murphy's character had to swam that English Channel and that's based off the information the film shown in regards to the mole story. And it had to been sometime between their 2nd day to before the day of Dawson's ship leaving.
movie was ass 
