1. Cillian Murphy's character was ALREADY on the yacht by the time Farrier (Tom Hardy) shot down that 2nd fighter (and accidentally shot the boat up that Tommy, Alex and "Gibson" was in). In fact, Dawson and his son saw the 3 spitfires AFTER they picked up Cillian Murphy and Peter, his son, put him in the cabin. As you said, Farrier's story was only an hour long. Cillian Murphy was already ON the boat by the time Farrer's story even BEGAN.
2. I think you are losing track of time. The TRUTH of the matter is that the majority of everything that happened occurred during the DAY OF Dawson's story. What we know prior to this was:
a.) Tommy, Alex, and "Gibson" able to get on the destroyer on that supposed 1st day. That destroyer was sunk by the torpedo from the U-boat, they tried to get on the row boat that Cillian Murphy was on and was denied (except for "Gibson" who was already on the row boat, and "Gibson" tossed Tommy and Alex a rope to hold on as they return to the beach.
b.) That morning, day TWO, we clearly see the row boat making it back onto the beach. So Cillian Murphy's character was BACK at the back as well. We also, see the conversation between the Army Colonel and the Navy Admiral where the Colonel fussed about where the destroyers and the Admiral told him they won't be another one in quite some time, due to what happened that night prior and the British military is taking their priorities elsewhere leaving them with one destroyer to come at a time and they have to rely on the civilian volunteers and their privately owned boat to help them across. We ALSO SEE soldiers, desperately and UNSUCCESSFULLY trying to use their row boats to get back onto the English Channel but the tides were to rough for them to get on. Those two things strong implies that Cillian Murphy's character COULD NOT HAVE gotten on another ship or even another boat for that matter.
c.) Between a speculated days 2-5, we see Tommy, Alex and "Gibson" shytting there on the beach bored and hopeless not knowing what they're fate would be. We DO NOT KNOW how long this part was.... But considering the timeline of them following the soldiers that found the abandoned ship was on the same day as Dawson's story started, it is reasonably believed that Alex, Tommy, and "Gibson" was sitting there on that beach for several days. And it means that Cillian Murphy between those days SOMEHOW left the beach and the ONLY PERSON we actually saw leaving the beach was the man that walked right into the English Channel. And these are all FACTS that happened in the movie. There was no OTHER WAY Cillian Murphy would of made it back to the sunken destroyer unless he SWAM there. The question is when exactly, it could of been in between ANY of those days.... it could of been immediately afterward they returned to the beach, or that day before Dawson's yacht left. it was definitely between those days and he just sat that HOPING a ship would come for him. As I said before, ALL OF THEM were desperate to find ANY MEANS to get off that beach. Nobody was trying to wait for another destroyer that in their minds wasn't going to come. It is the same reason Tommy and them following those other soldiers outside the perimeter to that abandoned boat hoping they could float on out there.