I guess there are some hidden feelings and misunderstanding that are causing mixed feelings.
Yuki is not a talkative person, she's evolving in this thanks to Naruse, but she's still working on that.
Naruse is a total revolution in Yuki's life about feelings (feeling it, expressing it, trusting a person totally, giving it all). She's experiencing some hard revolution and she's changing gradually. Plus, the more they're together the more she let herself be into him, her feelings are growing together with the wish to express it, even if she's still not the best at that. More than this, Naruse that was always the right guy, in the right moment, no misunderstandings, no shields, he always understood her behind her silent and he always reassured her with no need for her to ask. But since he got into university he's experiencing some new emotions, insecure, jealous.. and I think Yuki wasn't expecting it. More than this, Naruse feels actually a bit guilty towards his ex, cause as she said, he didn't love her.
So, I think it's legit for Yuki to be jealous and ask herself "did his ex actually forget him?" and "what if now that he matured he can be brought back with memories, drag by regret and what ifs". It's not that she doesn't believe that Naruse loves her, she's just insecure and not yet fully able to manage such feelings, of both love and jealousy. She's never seen Naruse help a girl willingly. When Naruse's friend kissed in high school he quickly settled things, here is different. He's letting his ex depend on him, not because he's unfaithful, but because he matured and he felt that he lacked as a boyfriend and as a human with her back then. He feels sorry and guilty and he's trying to be a good friend.
Naruse sees his ex as just an ex, because of this he never thought about how Yuki could actually feel hurt from this situation, simply cause he doesn't mean anything deeper and so he does not think Yuki could see it this way. Naruse knows his love for Yuki and his non-feelings for his ex, that's why he can't really understand why Yuki was so angry about all this, cause for him it's nothing. Not even worth to be thought, not a hint about it, cause he's just generous, genuine and he loves her endless, so he didn't even think about to see deeper into the hug/support matter. Again, I don't think Yuki doesn't trust him, she's just jealous, insecure and understood his sentence differently than how he meant it. And his ex is acting totally fine too (she still has a thing for him but she runs infront of him to not meddle between them)
Naruse is experiencing new feelings. He is facing his past with different eyes, he surely blamed himself for not knowing, not caring enought for his ex at time, he's some kind trying to repair what he thinks he wronged. Also, he's always been the ace in high school, even thought he was younger than some of his teammate. Now not only he's not that special in the team, but also he experienced the enormous progress of his rival. Naruse is for the first time insecure too, and this made him focus less on Yuki's insecurities (on contrary than before), and this had an echo on their relationship. Not that he's to blame, just we started with Naruse being the cause of a Yuki development in her personality, where she had to destroy some point of the old her and grew up, building new ones. Now is Naruse's turn to do that, but both of them didn't get it yet.
Naruse understands Yuki very well, that's the reason why in the past he was always able to settle her insecurities, even when she didn't speak them out loud, that's why I really love him. I think right now in the story, due to all the changing he's been trough (University life, also in the team, Hakamada, discovered that is ex was in a miserable situation all alone and he didn't even care enough to find it out at the time they were together) he's not lucid as usual, so he can't really see clearly like before, through Yuki when everything was fine. Does this makes him a bad boyfriend? No, it makes him human. But I also think not even Yuki can see all his fregilities in this moment.
Naruse was always the one that stabilize the couple and understand her unspoken. But he's growing as well now, he'll have his "eggshell ground to walk on, he's insecure and all what was said already, and I think it's a good thing, cause he couldn't be the stabilizing agent of the couple forever, that's not a healthy couple dinamic.
Naruse is also feeling jealoue of Hakamada. There's nothing wrong in Naruse being jealous of Hakamada. This is human-like as well. And because he got jealous. For the first time he didn't stop there and didn't think "how's she acting like this? Did she get the wrong meaning of my words? What are her feeling right now?". Maybe he'll think about this later. I guess he wanted her to say out loud her jealousy, "is it OK with you?" he said, and she hurt him saying "sure". But Yuki didn't really mean it. And I think that's because Yuki tried to not be jealous, she didn't want the jealousy to be the reason of the discussion, so she didn't talk about it. She thought that he couldn't share it with her, but that's not what he meant, and we see clearly his cluelessness on his face at her reaction. And he also recalled Hakamada. Probably Naruse was already suffering from their distance and the fact that she got mad made him think "you mad at me for such a stupid matter when you speak to him so normally? When you smile at him?".
So there's all these misunderstandings and they couldn't overcome them at the moment like usual cause they both are instable and more insecure and fragile.
They just need to talk the whole truth out. I can empathize and understand both of them, and when they'll realize everything they'll feel really sorry. I'm sure that this will make them grow as a couple. ^^