Why Is My Dog Pooping In The House Even After Being Outside? Potty training puppy problems. Obviously when your dog keeps going to the bathroom in the house, most of the time this involves puppies who aren't fully potty trained, but, puppy ... Your schedules aren't lined up. Alternatively, it could just be that you haven't figured out your pup's schedule yet. ... Your dog may be anxious. ... Underlying medical issues. ...