Not when they poop. If you see the little problem icon lite up (the bottom right hand corner) and you pets in perfect health and everything, thats uaually when your pet needs to be disaplined. The icon should go away after that. That's what I do and it works.
You can also pody train your pet. But it has to be done when it's a baby or when it's a child. If you see little "smell waves" on both sides of your pet, take it to the bathroom and you'll see it use a poddy. The poddy will look like a duck when it's a baby and it will change into a regular toliet when it gets older.
I hope I didn't confuse you! XD! Pm me if you have any more questions and I'll do my best to help.