In a late-game cutscene, the game shows the faces of Bear and Major Edmond when it is obviously Prince Thrakhath who is speaking. Was this bug in the original release as well?

I can't speak for Wing Commander 2 Special Ops 1 since I haven't played that part of it yet but I noticed the CPU settings for Wing Commander 2, at least in my case, made the cutscenes act odd. I would suggest opening up the dosboxWC2.conf and changing the cpu cycles to about 4000 or 5000 and see if that fixes the problem.

i cant even get the special ops even though it was supposed to be part of my bundle what gives

Yes, it was. Funny, no one corrected this for last 20 years... :-)
(in fact, faces are chosen semi-randomly, I've seen almost half of the cast in this cutscene over the years)
SO1 has plenty of bugs in its cutscenes.