Maltese dogs need to stay with the mother for 12 weeks or longer. If you got your puppy before 12 weeks that could be a problem. It is between 8 to 12 weeks where the mother teaches her pups about proper house behavior not to mess where they live. I had a rescue Maltese that I got from a shelter, that never did grasp the whole house breaking task and we had to watch her closely. The good thing about her she would not mess in any human bed, which made the night safe from land mines in the dark. This maybe the case with your baby.
If you run a computer search about house breaking a dog there will be over a million entries so you are not alone.
You might try northcentralmaltese.com they deal with Maltese dogs and will be able to help you. The great thing is Maltese Dogs are the best dogs in the world so good luck