I just noticed I'm having this problem, too, with the food bowls disappearing from the automatic feeders. It's a game I've been playing since January or so, where I have several active families that I rotate with. The family with the problem lives in Forgotten Hollow, the other families I play live in Willow Creek and Newcrest (so no connection the apartment living issue of disappearing objects).
At first I thought it was because I have 4 husky ghost dogs that appear at night on this lot (thanks to my "pet cemetery" on the grounds) and I know when they were alive they liked to carry bowls around when hungry (the regular ones, not the ones from an auto-feeder) so I figured maybe they stole them when I wasn't looking and I'd find the bowls later; so I bought new bowls for the feeders.
Now a second night has come and gone and the active (alive) dog in the family was complaining he was hungry. So I checked and both bowls are missing from the feeders again. The ghost huskies were there flying around, but I didn't see any of the ghost dogs with a bowl in his mouth.
My Sims in this game have never lived in an apartment (which I heard had some relation to disappearing objects), and I don't see any random dog bowls just laying around the lot away from the feeders.
I do not know yet if any of my other families in the other towns have this issue, too, but I will go double check. Like I said, I'd been playing this file since January and only noticed the missing bowls a couple days ago.
Thanks! :-)
CC
ps: My game has no CC or Mods, and I have all the packs and updates installed. (Win 10)