Early in Final Fantasy VIII, Squall and Quistis's relationship is a little strained and uncomfortable on account of bad behaviour. That's well established; Squall's 'go talk to a wall' line often comes up in discussions of Final Fantasy VIII.
This may be a little more controversial, but I don't think the bad behaviour is only from Squall's side.
Considering that Final Fantasy VIII is unvoiced, there's some surprisingly effective use of silence. The dialogue boxes are sometimes timed to make it clear that there are significant pauses in a conversation, even if those pauses can't be 'heard'.
This particularly stands out in Squall and Quistis's early interactions. There are pauses where Squall analyses the meaning behind what she's actually saying; there are pauses where he decides how he's supposed to respond to her flirting.
Squall is uncomfortable around most people, but, at the start of the game, he seems particularly uncomfortable around Quistis. And, honestly, he's got good reason to be! Quistis is in a position of authority over him, as his instructor, but she's inappropriately personal in the way she behaves around her student.
It's clear that their relationship as teacher and student is on Squall's mind when Quistis flirts. When Quistis approaches Squall after his dance with Rinoa, he brings up the fact that she's his teacher the moment she implies that their relationship is too impersonal:
Quistis: You really are an excellent student. Even that dance was perfect.
(Long pause.)
Squall: Thank you.
(Long pause. Quistis isn't leaving. Squall sighs.)
Squall: Yes?
Quistis: So you'll dance with someone you don't even know, but you can't stand being around me?
Squall: ...Whatever. You're an instructor, and I'm your student. It's kind of awkward when you don't say anything.
Squall is often criticised for being rude to Quistis in the early game, but I have a lot of sympathy for him. His teacher is being inappropriately personal with him; I can't blame him for trying to set boundaries.
Am I too inclined to take Squall's side because he's my favourite character? Yes. You can't stop me. It's my website.
To be fair to Quistis, I can understand why she wants to treat Squall like a fellow student. She's in a slightly lonely situation; she's only eighteen, but she's divided from her peers by her role as an instructor, making it difficult for her to spend time casually with people of her own age. But, at the same time, I can understand why Squall is uncomfortable with his instructor's efforts to get closer to him.
Of course, this strained dynamic between Squall and Quistis only exists in the early part of the game. Later in the story, the two of them develop a close bond as allies.
In writing this page, I'm not trying to argue that Quistis is a bad character, or that there's anything wrong with liking Squall and Quistis as a pairing. I mainly wrote this because I often see people saying that Squall's early behaviour to Quistis is inexcusable, and I wanted to offer a different perspective.
When Squall tells Quistis to 'go talk to a wall', he's definitely being unkind. But, if you bear in mind what's led up to that moment, it becomes clearer why Squall is trying to keep her at arm's length.