Anonymous, they are very intelligent and the "clean" part is within ferret
limits.  If the litter pot's use is not obvious then accidents will happen.
If the litter is of an unacceptable type they will.  If the litter pot is
too dirty then the ferret will go elsewhere.  If the ferret is in too small
a cage or having too little exercise then frustration will occur.  Outside
the cage, through the years with many, the over-all hit rate for pots has
been about 80% because most ferrets like to do some scent marking and they
do some of it with their waste.  This is normal behavior for the species
and you get around it with more litter pots, plastic runners, newspaper,
and patient training to reduce the incidence rate, but largely you put up
with it.
 
Using bathroom habits and thinking that they have to be the same as a
human's or a cat's for a ferret to be smart just doesn't cut it.  If that
had been the case would Steve have been able to say several times to
Meltdown that she should Get Warpie and then get treat -- then put Meltdown
down to have her climb under the platform bed and then climb back out
dragging Warp like a kit by the scruff, deposit Warp on Steve's foot and
look Steve in the eye then lick her chops?
 
You need to realize that critters have their own species' behaviors like
scent marking and that not only do the animals bend to what the humans want
(which is very intelligent learning) but to some degree the humans have to
also be intelligent enough to bend to what the animals want.  Fortunately,
your post indicates that you are and that figuring out why it is happening
is possibly all you need; not all humans are as gifted, though, so some
can't modify their behaviors to fill the needs of ferrets. :-)  In ferrets'
cases this means coping with the scent marking.
 
Who told you that they are incredibly clean?  A pet store sales person?
Hey, there are good stores and bad and good sales people and bad, but the
run-of-the-mill pet store sales person we seem to read about here fits the
used-car salesman jokes of the 1950s and 1960s, and does so a lot better
than any used car salespeople.  Whether the bad ones just are more likely
to be described here, I don't know.  It's likely.  I was in retail sales
before I returned to college -- managed sales as an adult and grew up in
luxury sales, actually, and I used to fire people if they used
misrepresentation as a sales technique.  It backfires on stores by
undermining confidence.  It's a big sales no-no right up there with
rudeness, clerkish behavior, or opening a conversation with a question
which can have a "yes/no" answer if there is an alternative.
[Posted in FML issue 3061]