Files missing in Time Machine

Yesterday I had to refresh some local folders on my MBP from a version control system that my company maintains.  Before doing so I had copied my working copies to another folder then after the refresh copied the files I had been working on back to the original folder.  I then deleted the second folder, thinking I no longer needed it.  This morning I realized that there were several image files that I forgot to copy to the original folder from the second folder.  I figured, "no problem, I've been using Time Machine since I switched to the MBP from a hated Windows PC in December."  I opened Time Machine and navigated to several backups from prior to yesterday but those files are nowhere to be found.  Do I just not understand how Time Machine works or is there a problem here?  There are other image files in the folder, just not the ones that are missing.  It appears as if when the files were deleted by the version control refresh yesterday it went back and deleted them from TM, which obviously makes no sense.

I have a similar experience:
Nearly the same thing happened to me, too.
iMac 27" mid 2011, OSX 10.9.1., external HDD directly connected via Firewire and exclusively used for TimeMachine.
Came to work on monday, booted up the iMac, computer got stuck at the twirling colourful beach ball.
I booted the recovery mode and choose the last backup from late friday.
It worked, but a number of my apps don't remember that they are licensed and some preferences are forgotten.
But that is just inconvenient. I discovered that some files in folders on the desktop are missing. And the last backup in my TimeMachine with these files is more than 1 month old! Everything newer is missing in these folders!
And I am very sure that I did not delete these files because guess what I was working on the last workday before this incident...
I am almost anxious to check all my data - who knows what else is missing!
I checked the exclude list in the system preferences panel and in the plist-file - no, my desktop is not excluded.
Any news on the buggy TimeMachine?

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