The biggest point of contention between Sansa and Jon has always been the importance of titles. To Jon, a boy who grew up as a bastard and never liked his title in life, they mean nothing and it's all about the greater good. Which is admirable, when you ignore how important titles are to other people. Like Sansa, who knows that titles mean power and allegiance.
We see that difference in action when the two clash over Jon's decision to bend the knee. Jon is adamant that it was to save the North, but Sansa points out how the men of the North swore allegiance to Jon and it's one of the few things holding them all together (as seen when Lyanna jumps to chastise Jon for his decision), and with him no longer King in the North, it's going to be even harder to keep them all united. She reveals that their bannermen are withdrawing because of his alliance with Daenerys, which puts their army in danger of getting even smaller.
In the same conversation, Sansa asks the big question. Since he made the decision to bend the knee, Jon has stated that he thinks Daenerys will be a good queen and it's vital to ensure the North's survival. But Sansa openly admits that she finds it hard to believe and asks him if he bent the knee for the North or because of his love for Daenerys.
Now a lot of people may find issue with this because Jon is nothing if not a righteous man, but the truth of the matter is, Jon bent the knee after Daenerys already agreed to help with the Night King. He didn't have to give up the North's independence since she was already set to provide aid after seeing the White Walkers and losing Viserion. So his reasoning doesn't really hold up water, which Sansa can sense. And if she ever figures out the sequence of events, she would rightfully tear him a new one.