I don't consider the traveling a plothole. I think the show is just kind of bad at showing the passage of time(or transitioning between certain locations), especially when the characters are traveling between places that are nowhere near each other. Sometimes it seems that only a few hours have passed in the episode, but then a character says something or something else would be happening that would imply it was days(or definitely more than a few hours) that passed. I'm not sure if that's the kind of travel issues you're talking about though. I don't remember anything too unexplainable/implausible with the bodies, except maybe the totem pole of bodies I guess.
I'm not sure if I'm remembering correctly(and I don't remember specifics), but towards the end of the season, Will was loosing time or out of it a lot. Hannibal knew that, so I think it was more a matter of him knowing that Will would loose time eventually, and taking advantage of it after the fact, rather than him knowing exactly when/where it would happen. It might have been a bit convenient for Hannibal that Will was out of it when he was, but I don't consider that type of thing a plot hole, and they also probably haven't explained some things yet.