Among the multitude of other issues, many of the choices I made were incorrectly saved and as such, the outcome of the game is (presumably) radically different from what it was supposed to be.
I chose to defend Duck in the pharmacy. At the end of episode 1 it showed the choice statistics and implied that I sided with Larry. Throughout episodes 2,3, and 4, Kenny says I sided with Larry. In episode 5, however, Kenny acknowledges that I sided with Duck and at the end of the game, it reported that I sided with Duck.
I saved Ben at the end of episode 4. In episode 5, Ben was missing. At the end of episode 5, it said I let Ben fall.
I shot Duck for Kenny. At the end of episode 5, it said I left Duck in the woods.
Most importantly, I chose not to take anything from the car at the end of episode 2, including the sweater for Clementine. The statistics shown at the end of that episode corresponded to this as well. Episodes 3 and 4 also reflected this. At the beginning of episode 5 during the "previously on the walking dead" montage, it shows Clementine wearing the Brooklyn sweater from the car when we were on the train (she wasn't wearing it when I played episode 4). When the stranger who kidnaps Clementine argues with Lee, he says we stole the things from his car.
This is in addition to the hitching issues and not being able to progress passed episode 1 without having to copy my save to the empty slots several times. I'm not sure if that "fix" is what caused this issues somehow.
Needless to say, a large part of what makes this game so excellent is the story and how involved you become because the decisions you make affect the outcome. The ending of the game was more or less ruined for me as it felt like many important choices I had made throughout the game were invalidated. Had I known the game was this buggy, I definitely would not have played it (at least not yet). I'm also concerned that when/if more episodes are released in the future that I'll either have to continue with the incorrect choices or replay the entire first 5 episodes just so that my correct choices are reflected in the game.
This really is a great game but I feel robbed.