Did you add any members after Friday evening (PDT)? If so, it is most likely the way roster lock works. Example: If you had 5 members Fri, and added 1 Saturday morning, when you play the war, only 5 members wins will count, even though your clan size is 6, and all 6 are playing together getting wins. That is normal, and is meant to keep clan wars fair, although it does cause confusion. See here for more information about roster lock: Clan War Division Brackets and Roster Locks
It's also possible that it may have nothing to do with roster lock, e.g. latency in wins being recorded, offsetting of wins on nodes held by a defending clan, or your own members joining your game and being on the other side, etc.
If you can rule out those possibilities, then the reason is easy, and I can some it up for you in one word: Beachhead
Good luck in your war, I hope you get your issue figured out.
Thanks for the response jnikoley, and all of your answers are right but I'm leaning towards the Beachhead. I'm familiar with the Roster lock and on Fri, around 5, I am done with it. Went into the war with 8 on the roster. (Locked) and added some guys back on the team after that but I was only expecting 8 to register. Had 2 teams of 6 playing, expecting 8 wins per game, we were getting 4. No Biggie. We still came in 2nd even with the broken scoring BUT I hate being cheated by a Glitch. Thanks for the response though.
Sounds like it could have had to do with roster lock, but thats just my guess.
Its a good idea to wait untill all 8 of your members earn a win before adding anyone back to the clan.
I also suggest doing your cuts on thurs, just to be safe. Dont trust the rumored roster lock time, assume it could be earlier.
If you want to play it extra safe, do your cuts one day early, and add guys back after the war ends.
In any case, congratulations on your second place finish. Good luck in your next war.
As far as I know issue with the scoring last clan wars were resolved. In that case, all scores on then end were final. Good luck
to you and your clan on the next clan wars. You can follow the suggestion of jnikoley . Good luck.