I happend to have experienced the same bug as Paingod, it seems, playing XRM.
I boarded a Pirate Centaur in HellForge ( i had 15 marines on board of my Wolf, iirc ). Then i´ve collected all the marines in space, using Toucan TP ( one of them appeared to be a "passenger", though, when trying to transfer him to another ship, i showed "stars" ).
Then i tried to sort my marines, after they´ve repaired the capped Centaur.
I could transfer them from and to Wolf <-> Toucan, but i couldn´t move them from the Centaur. I noticed then the doubling effect ( luckily, Paranid names are short, and easy to remember ). I needed the Centaur for some mine towing actions, so i didn´t sell it right away, and when i was boarding a Boron Thresher recently, in the property menu where you can see your marines fighting, i noticed the those "doubled" marines seemed to participate in the boarding operation.
Now, i´ve found out, that i could transfer marines from Elefant to my Split M2, and the doubliing effect occured with some of them ( obviously those i´ve picked up in space in HellForge, but then i´ve transfered them back, and when i tried this again, the doubling effect dissapeared.
So, the only doubled marines i still have are those on the Centaur. Since the Centaur has only place for 8 marines, and it was full, so i couldn´t transfer them back and forth, that seems to me a problem. Gonna sell it, and if the marines dissapear, i´ll have to cheat me some instead, or i´ll just live with the fact they´re gone ( kind of MIA ).
@Dr.B: Note, i haven´t ugraded your boarding tool to the latest version, since my game seemed to be stable, so i must have the one before you included the spacewalking marines repairing ships, i think
Edit: i´ve possibly should have posted this iny your marines thread, Dr.B.