Same issues. All my choices in both my saves were wrong but identical to each other, as if they had been merged.
Copied the one I knew was my main then deleted the original. Choices from ep 1 and 2 corrected themselves, but 3 was still messed up. Restarted the ENTIRE episode 3. When I finished, checked the stats again. Episode 1 and 2 stats changed again and are now wrong but ep 3 was okay. Started ep 4 just to see if the stats were just showing the wrong thing, but my choices were okay, but it was immediately apoarant that the ep 1 and 2 data was wrong.
Restarted the game but decided to hold off for a fix.
The game is 100% about my choices and I'm kind of pissed that mine is messed up. Don't want to play until there is a fix that doesn't require me to spend days replaying all the previous episodes.