Yes, this is what happened to mine. That's likely data that was from un-refreshed dungeons.
My game has been working flawlessly. I stopped visiting dungeons once I noticed they were linked to the rapid increase in file size (I posted a thread letting everyone know but it didn't seem to be accepted at the time) so my file size stayed reasonable despite over 40 hours of gameplay (currently 4.4 mbs). The only thing that's happened that I can't explain is I hit an enemy with an arrow in the woods and he must have been knocked out of sight because I can't find him anywhere.
I did the same thing as you. Until the patch came out I stuck to the Whiterun area only and kept my inventory as low as possible. My save file stayed around 5MB. I did do some dungeons but I only did the ones already in my journal. And I cleaned everything out of them after I cleared them. I also try to avoid exploring dungeons unless a quest sends me there. Less chance of them glitching if they are done in the order they are intended to be done.
I've also had creatures dissapear after killing them. lol
You must have knocked him into Oblivion!!
Only weird thing I've had happen is during the Mage quests. When the arch mage gets thrown outside after trying to stop (Arcun is it?) who messing with the eye of Magnus. When I go outside to find him, he is dead (which is suppose to happen) but half his body is stuck in the ground and I can't search his body. But I know he isn't carrying anything. I checked before he died.

Good luck!