User blog comment:Pawn of Atlas/Important Discussion for Rapture Storyline page/@comment-24171094-20140329114206/@comment-24171094-20140329121852

I understand what you are talking about. It's strictly contradiction. But, wikia people filled up that gap with logical(?) explanation( look at the Storyline or Andrew Ryan page etc ).

Anyway, That FF logo from Bioshock 1 is Fontaine's head logo. FF logo from BaS is atomic style design logo of Bioshock 2.

Furthermore, there are more references:

-1) BaS Splicers wear boxes, and one of the box is Hop-Up Soda. Actually, it was introduced first in Bioshock 1. But, title phrase and poster and logo was invented in Bioshock 2.

-2) One of BaS Splicer's mask is from Meal-Time Frozen Dinner poster which is first introduced in Bioshock 2