I had this happen recently as well and I'm sure it has happened before but was too overwhelmed with other stuff to notice.
Here's the crazy thing. In my case I was double recording into two tracks simultaneously. They were in a folder with the record mode set to Group all Clips in Folders. It was guitar parts recorded using the dual output of my amp so I wanted to be able to easily edit both sets of clips simultaneously.
One track all the clips/lanes went sequentially from top to bottom. In the other bottom to top. Very strange, confusing and silly. I was going to start a thread to see if anyone else had experienced this or if I screwed something up. You seem to have confirmed the quirk.
I cannot be certain if they recorded this way or if, like in your description, it happened sometime after the fact (as in they recorded in the same order then one set of lanes did a backflip at some point afterward).
Cheers.