Bitty is a gay man in a collegiate sport who grew up in the Deep South. He is Aware™ of himself at all times, even if he doesn’t talk about it on his vlog. He probably knows that although he is accepted now, if he crosses an invisible line of physical/emotional affection with some of the guys that acceptance can disappear in an instant. We can speculate on the sexuality of the other guys, but none of them are open in the way Bitty is, so he has to operate on different rules than the other guys.
We know, canonically, that he is mostly exempt from rough-housing. This isn’t because he’s smaller, it’s because he’s gay. Rough-housing is toeing that line and Bitty would probably be careful to exclude himself whenever possible. The other guys probably exclude him with the excuse that he’s small, but there’s a layer underneath that they would never acknowledge. This is the sort of thing that even really supportive straight friends do, often unconsciously. It’s part of the “unwritten rules”.
So, back to Jack. We’re shown the two of them getting increasingly touchy in the background of several panels Year 2. We’re shown through Bitty’s twitter that Jack seeks him out, incessantly chirps him (which by Bitty’s own admission, is a variation on flirting), and starts to include Bitty in the rough-housing. Bitty overheard the conversation with Parse and heard Parse interrupt Jack with what was probably a kiss. Bitty can connect those dots – he’s not dumb. The thing is – he’s also never going to bring it up, because Bitty understands living in the closet and how scary it is. He also understands that Jack’s future is on the line. Jack already has so much stacked against him – the overdose, the crazy expectations, his own crippling anxiety – and Bitty surmises that Jack can’t also live with his sexuality out in the open too. So, he lets Jack get closer, orbiting him, but never, ever pushes him or even hints that he knows. It’s a secret and Bitty isn’t going to violate that.
Instead, he just cherishes the moments he gets. He catalogs them carefully, even though it probably really hurts. The guy he has an outsize crush on keeps seeking him out and sitting too close to him and giving him piggyback rides and lending him his jacket. Bitty knows that this is outside the bounds of his other friendships. He knows that Jack is crossing the line and he lets him, instead of closing himself off and not allowing it like he might have with the other boys. He just shakes his head and says this boy.
What I’m getting at here is that Bitty might have known, or at least strongly suspected, that Jack had non-friend feelings for him. However, he also probably thought that Jack didn’t think they were important or big enough feelings to actually act on. That’s why we find Bitty literally sobbing in Jack’s room after graduation because Bitty thinks that it’s the absolute end of the road for them and even the casual flirtation will be gone as soon as he boards that plane to Georgia in a few hours. Jack is moving on to Providence and the NHL and Jack isn’t going to take the risk on his future. Bitty wasn’t expecting Jack to kiss him, but not because Bitty was oblivious to Jack’s feelings. He doesn’t expect the kiss because he has convinced himself that Jack does feel something for him, but not strongly enough to actually pursue it.
ETA: now in 5k-word fic format, for your angsty needs