I have chosen the picture in which his hind paw is obscuring the poop from the camera because oh come on. Anyway, here isw Sora, scratching the BARE FLOOR in an instinctive attempt to cover the poop he has left behind juuuuust barely within camera range.
Now on to the harder part of the issue, which is trying to figure out WHY. I think we can rule out crystals in his urine because (a) he's left no pee behind on any of these incidents and (b) they're being fed special anti-crystal food. It's probably not that he wants a cleaner box, because it was very recently cleaned. It may be a territorial thing, or he just may not like the box in its current placement.
It might be significant that the other box, which is in the spare bedroom, has had no similar incidents.
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