I have had this bug too and I don't have mods, CC or EL.
I was really worried the first time my sim's puppy disappeared, since her house has foundation and I just couldn't understand where the pup could be. Later it happened with Catarina Lynx's cats too. Luckily my sims have always been able to call their pets and they have returned.
I agree that it's likely that the bug came in the pre-ep update, because I think I started to experience it after that. I looked at my screenshots and the first time my sim's puppy disappeared was probably the 20th of June. I think it was also the first time, after the pre-ep update, I played a sim family that has pets.