Part of it is just their personalities. Jon is a bluff, honest, no-bullshit guy who hates politics and maneuvering, and Littlefinger is everything he dislikes - dishonest, slimy, always has an ulterior motive, everything that comes out of his mouth is a lie or a half-truth. A person like Littlefinger is always, in any universe, going to give a person like Jon the creeps.
And then there's the uncomfortable fact that Jon owes absolutely everything he has to Littlefinger, which is a terrible position to be in if you're trying to be the independent Kinginthenorth. Nobody likes owing a massive unpaid debt and having no idea what the terms are, and especialkly nobody likes owing a massive unpaid debt to a man who may be Cersei's stooge or may be about to try to take the Iron Throne himself. Is LF going to assassinate someone per Cersei's reuqest, demand that Jon bend the knee to the new King of WEsteros, or join in a campaign of conquest? What will happen to Jon and the North if he refuses such a request, will the Vale knights wipe him out and doom humanity to a zombie apocalypse?
And there's his giving Sansa to the Boltons and then wanting to marry her himself, which is mega-creepy. Jon has every reason in the world to dislike and distrust littlefinger, and to wish him gone to the south.
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