Does he have diarrhea or soft stools? What are you feeding him? I can't imagine a 18 week old pup making that much of a mess. My pups that are that age have very firm stools so even if they walked in them it would not create that kind of a mess. Lucky for me mine go to the far end of the x-pen to do their business on their potty pads.
You might try laying his bedding by the gate and his pads away from the gate and see if that would help. I am sure he is just very stressed from being alone all day. Perhaps someone else will have good advise.
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