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I have a question. The dungeon that you are doing the mission in, does it have any water? That might be the problem as well.
Water type Pokemon can walk on water, and this makes things tricky. Unless you can walk on water too, you might not be able to find the Pokemon in question, and even if you do, it might take forever for it to come close to you if you can see it.
I've had this problem happen to me a few times, and it's kinda annoying. If the dungeon doesn't have any water, then just do as suggested and try again the next day.