I'm not aware of any inconsistencies in game at this time.
The one that inspired me to make the comment was this: Lin mentions that she meet the revolutionary lady when she was being auctioned and revolutionary lady kind of confirms this, later on it's shown that Lin was a slave and actually meet the revolutionary lady during the industrial age while doing some task for her master.
Will be making a list of the rest (Most of them are related to continuity issues, like Cornwall mentioning the previous challenge, which was removed and replaced with Cornwall political discourse, or Felicity and Emma not recognizing you in Ashley story even thought they were already moved in the hotel).