I am not 100% certain, but I dont believe this is a bug. Each mission is independent, facing a character in one doesnt exclude them from being in another mission where they are an option.
Last year a forum post listed which bosses could be encountered during which battles. Some bosses could appear on multiple battles - yes, also in the same zone (vertical slice). I won't dig up the post again but the recommendations in this link supposedly make sure that you don't encounter hard counters to the team you're using (that's the idea at least):
I believe you cannot encounter the same named character twice in the same battle (if you face a non-elite Fives in wave 3, you will not face an elite Fives in wave 4), but I've definitely faced the same elite in both missions of a single territory multiple times.
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