I only have problems with the pets who have been trained or nearly trained to be destructive and pee inside and so on. The rest seem to quickly learn what they should do and behave fairly well, whether or not they've actually got the skill. I do have chewtoys and scratching posts available for the more destructive urges. My Sims just Praise or Scold as appropriate when they get home from work and everything's copacetic.
I do use the cheats that make pets controllable (so I can force them to eat if necessary, then Praise them) and make their actions cancellable (in case of a mid work shift furniture scratching orgy).
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