I see a fair number of rusted nuts + washers on unrusty bolts (presumably stainless, or some look to be galvanized). I think I remember seeing a wedge bolt distributor's description of their stainless bolt paired with a carbon steel nut, but I can no longer find it. Or perhaps I'm misremembering.
So: is there an engineering reason why a non-stainless nut + washer would be paired with a stainless stud?
No there's not an engineering reason for this, at least not a good one in this context. Pictures would be helpful. It's not uncommon for the washers to be lower quality than the bolt and start corroding first. Likewise it's not uncommon to have the nut rust before the rest of the bolt starts to rust. If the bolts are actually stainless perhaps someone just mixed up the nuts with plated steel ones. I've encountered bolts that the nut/hanger was removed or fell off and was replaced with whatever nut someone had on hand because it was better than the bolt missing a hanger.
Not a great picture, but the stud itself isn't rusted. On this route (from 2010), this is the only bolt on which the nut/washer are rusting.
I'd always assumed that, as you say, such mismatches were accidents (or maybe someone trying to save a few cents) from either the distributor or the installer.