When playing HW2 Remastered, upon completion of a mission, any subcapital docked into carrier (with carrier set to allow ships to stay docked) will not be carried over to next mission. Lost my elite squads and entire wing of bombers before i figured this out.

Is this the same for everyone, or is it just me?

I had that problem too, one of the reasons I quit #2.
I looked around and never did find a fix but maybe you'll have more luck.

I can't comment on remastered, but in the original the transfer save is made in format of plaintext script (and I even faintly remember something alike your problem). There's a good chance it might be the same for the remastered. If so, with little research around you might learn to edit that easily.

That's ugly, I know, but that's a somewhat viable work around if nothing else.

Frankly, that's also how I ended up playing through the final part of the second's campaign myself, by designing my fleet in text format before the mission. Not because I wanted to cheat, but because I was fed up with some aspects of that game, and just wanted to see it trough, and have fun.

I really like the HW2 skirmish fights, much more than the first, somehow, but the changes they did on campaign mechanics and some aspects of the dynamic difficulty just failed on me.