Some files get deleted because they break the rules; ie hetero and bi porn. We don't catch all the rule breakers, but that doesn't mean that we should not delete the ones we do see.
As for files with different versions, it's up to the uploader to clearly state what is different about his upload vs another upload of the same file; ie file size, quality, format, etc.
Many times we get the exact same file but with a few pictures added so it makes the file size different than the well seed version that is already on the site.
Also, some people try to get clever and alter the name so that it doesn't appear to be the same file as one that is already well seeded on the site.
Without knowing the exact files you are talking about, I can't look to see why the file{s} you are talking about were deleted, but the above should give you some ideas.