This keeps happening to me. I open a question that has some VTC as duplicate. And I find myself about to upvote the question. When I stop myself, I have come to realize why it happens:
I am not sure what to suggest, but I do feel a little disoriented when I deal with these questions. Maybe have a link in the dupe banner that I could use to express my agreement (or disagreement, if we ever implement vote-not-to-close-in-parallel right from the question) would let me see the voting buttons as belonging to the question again?