I'm sure you did... though it might be you never realised ! If you still got a save state from the end of the 2nd chapter ( so at the start of this one ! ) you could realise again a small bug with the percent counter... you did finish at 4 % but if you start this one you get reduced to 3 %
Treasure of Nadia was funny as fuck at v92... I started with 91% and instead of finishing it at 92% I ended it with 89%



( although at the second run nothing similar happened so it's not clear what exactly is at cause

)
In general these " bugs " are not threathening the gameplay if you play it how you are supposed to... when you take a tour into " let's fuck up the game " you can have great success though !