I had the same (or at least similar) issue: A video taken with my iPhone 4S (running the most up-to-date iOS 6) would not play in Quicktime player, but it DID play in the Finder preview, surprisingly. I finally figured out what I did wrong: I first downloaded all of my "Camera Roll" to my Mac in iPhoto, then exported the files from there to a Finder folder. However, I didn't pay attention that the default export file type is .jpg - which is obviously not the right one for a video. So I went into iPhoto again, selected the movie file, chose "Export" and then selected "Original" instead of "JPEG" from the "Kind:" pull-down menu. (Stupidly, iPhoto reverts back to "JPEG" the next time you open it - why? Also, why is there no easier way to download picture and movie files from the iPhone to the Mac than the route I just described? But this is besides the point of this discussion...)
Anyway, now the video plays in all the right ways as intended. - might be something to try?