Does it have fleas or any sicknesses?
I've seen that too with the scared.
Was your dog sprayed by a skunk or did you go on an adventure with him ? Mine seems to have gotten back to normal now after a few days
Also if your dog is a glutton he may become uncomfortable by overeating. Exercise should help in this case.
Only limited testing done on my glutton dog but it seems to work. (Have to see if I can craft some medicine for it like a laxative)
I am having the exact same problem and somethings that I do help, but then it comes right back and is making me super mad.
I found the problem. Your pets have fears, and some fears are appliances and stuff like that. My dog was scared of the stove (so I hand to sell it) and other dogs have been scared of computers, tvs, other animals, ect. If you have problems with them being uncomfortable, just try and make your sim turn on and use stuff and see when your animal will go and cower somewhere in your sim's house.
There is also another possibility. If they were sprayed by a skunk then it will be uncomfortable until the smell is gone. You can see this by a "cloud" following them.
Bathe them often and it is gone in a few days.
There's also a bug with them being constantly afraid after getting shots at the clinic.
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