It sounds like he may be slightly malnourished. It is normal, however, for very young kittens to have softer stool than adults.
At 3 weeks old, he should still be with his mother. Even if he's eating solid food, you need to be feeding him kitten milk (which you can buy at a pet store) and kitten food. Wet food is better on the tummy at that age.
How did you end up with such a young kitten? Not that it doesn't sound like he's much better off with you, but he should still be with his mother and siblings.
Are you able to take him to a vet? He should get a checkup to make sure he isn't sick. You should also start deworming him. You can get deworming meds from the vet or the pet store.