The short answer? File systems can do that.
The long answer can be painful...
Bios check-sum error on a previous write.
FAT mis-calculation/error causes write to occur somewhere already in use on disk
File system crash while accessing the disk
Disk corruption in a location not associated with the issue, but during a repair, data is moved erroneously.
Disk corruption in a location associated with the issue, moved files did not have 100% data restored
You moved or modified a file in one of the directories
A bug in a patch that failed to properly update a file
... 1,000,000 more equally unlikely possibilities... Which makes trying to figure out why not so important (as it is very rare and usually requires the perfect alignment of problems for something like this to occur, and is far easier to fix than to diagnose).
And the best part is, at the end of the day, if it is just a corrupt file, it doesn't matter (except for the Disk Corruption or the you moving a file, as one may mean your hard-drive may be dying, and the other falls into the category of don't do that).