Are you saying that this kitten is UNDER 6 weeks old? If so then their habits are not necessarily formed yet. The litters of foster kittens I have had all learned at different ages not to miss the box. And a very small kitten may require more than one acceptable place to go potty. Houses are BIG when you are a wee kitten. And also remember that cats like to do #1 and #2 in SEPARATE places. She might be showing that tendency now.