Nah. Don't even sweat one drop. It's natural to assume the three, no, four games are related. Only the middle two, EAW and OP are. Unless you were one of those who snatched up SFC1 the year it came out and stuck with us here, at Taldren, and before that at the Simxtreme boards, it wouldn't be easy to figure that out.
Lots of people have asked what you did. I know I did, in the old boards. I got the same answers, though in those days, I think some were more hopeful that they could do it until they looked at both games in much more detail.
Keep enjoying SFC1; I think it is a jewel of a game and the one that started it all! I particularly love playing standalone Fed Hostile Skirmish (a stock mission script, but I take a F-CB with extra marines and max suicide shuttles and scatterpacks up against whatever three Klingon heavy cruisers they throw at me. On my old computer with Win 98, I toasted them always; now I have really cool rig I made myself, but with Win XP and SFC1 lags, so they mush me into a puddle of plasma.
), Surprise Reversed 2, Repair Rendezvous, Lyran Commerce Raid, Convoy Assault, Convoy Attack, Limping Home, Foreign Order, Orion Starbase Assault, When Opportunity Knocks, and a few others.
These missions should still be available on the Starfleet Universe site. It's a site with great stuff in it.