It always seems to assign either the / page or the // page to the supplemental result index in every instance I have seen it.
Are these pages going to get a duplicate content penalty?
Is this a true canonical issue or am I seeing something else?
Any idea what would cause it? In the instances I have seen there is no coding error (two sites though not my own, the respective owners have checked them as thoroughly as possible). Could it be an external linking error with someone linking to the wrong uri?
That can be a very bad sign, IMO. Either it would cause duplicate penalty or not, you are at risk of having your ranks drop or disappear. I encountered this issue since Oct 05 and the return of ranking is painfully slow about few pages for the some targeted term but not universally throughout the site as before.