I can only guess, but one possibility is that a file was saved, and then immediately after, a save-as was done. The time stamp could wind up the same in that case, and the file that was saved-as would have extraneous data (from changes and re-saves) stripped out.
Thanks for the answer. The issue is that I forgot which file I was finally editing and saving as a pdf. I will look at the files again - side by side..