@thofheinz
She messed up, did something that obviously hurt him, and at the end of their short conversation
he's the one saying he wants to become someone worthy of her affection.
That's why she's telling him he's "too kind". Ironically, it's pretty similar to what Iino told him last chapter, although expressed in wildly different terms.
Humorously, this is why I like Tsubame - once she thought about it, she was perceptive enough to realize how badly she'd managed to hurt him, owned up to it, and apologized. It became very clear that basically saying "I don't want a relationship with you, but I'll give you a pity fuck anyway" (or something Ishigami would interpret on those lines) was potentially the most damaging thing she could have said after his confession, given how Ishigami works.
Also, Iino interrupting them right before things potentially got even more awkward is one of the things I like about her. (There's no way Iino wasn't listening in on that conversation. Her timing was too perfect.)