Well I'm not quite sure what the person meant when he said it but I'll tell you what I think. I think this basically means the they are the perfect couple in the wrong situation. Ex: They are a match made in heaven but, their parents don't want them to get married or whatever so as they get on the plane to Mexico to elope he looks at her and says: "We are the perfect couple, just not in the perfect situation." I hope my mindless rambelings help!
It means that you are suited for each other and meant to be but just the problems you are faced with is nothing like the couple which is perfect and that things are not going as exspected though the two companions are perfect.