I think I found a bug in deleting "raw DVD rips" (IFO/VOB sets in a VIDEO_TS folder as you described) this past weekend, but I haven't had time to do testing to confirm.
But, since it came up... This happened to me this past weekend:
I was pruning some old, cruddy files out of one of one of my auxiliary MC Libraries. I was just browsing through a big View of "all files" filtered to one particular (large) dumping ground directory. I'd been deleting a lot of files as I went through the directory here and there. Select a few, delete. Select a few more, delete. And so on. Then, I selected one particular DVD rip that happened to be an IFO/VOB set, by itself, and deleted it (using the Delete & Recycle or Straight Delete from Disk option, I'm not positive, though I usually use the Recycle option).
MC put up an "Updating Database" please wait dialog. For a lot longer than it should have taken to delete a single IFO/VOB set of one movie. I ended the task on the Media Center process. Upon re-launching my Library was okay, but it had deleted 1.6TB of files from disk. It looked like it deleted only items I had in the "current view" in MC (like it started deleting everything in the View, not just the selected file). The files were not (none of them) in the Recycle Bin. Just poof, gone. The Library was full of broken links.
But, I don't really know for sure what happened. I was more concerned with recovering! Luckily these weren't essential files, and with the ones I had backed up, and the ones I could undelete (since I caught it) I only ended up losing ~400GB of stuff out of that 1.6TB, and most-if-not-all of that was junk anyway.
So... There might be some kind of bug with deleting the compound IFO/VOB file types? Or perhaps I screwed something up and hit Control-A right before I hit delete? I don't know at all.
But, if what happened to me was real, and if you were looking at a View showing only those two entries, then maybe?