I live on multi floors and have a pee pad trained pup. I have a pad on the first floor (laundry room) and on the second floor in her playpen that she sleeps in (it has a "door" that is left open in day).
Just wondering, do you think your little one could be marking? When we first got Gidget, she kept making a little pee patch on the "wipe your shoe mat" by the one door in the house. We think it was marking.