I'm frankly so annoyed about this.
How can an author have a couple of girls be useless lesbians when they literally already dated and even had sex? Like it's too ucking late to have them be all "oh, d-does she likes me?" You literally fucked of course she at least finds you a bit attractive!
It's so frustrating.
What Manatsu is unsure about is whether Nagi would want to become her girlfriend for real. She is afraid to ask Nagi out because she's afraid of rejection. And from her perspective, it would not be meaningfully different from rejection if Nagi told her she
only found her attractive enough for sex. The idea that what they had wasn't as special to Nagi as it was to her is scary enough to discourage Manatsu from getting a straight answer.
As for Nagi, she explicitly set the limit as seven days so that they could stop before things got "complicated". Falling for Manatsu seems to be exactly what she was afraid of. On top of that, she could tell from the start that Manatsu was attracted to her. (Unlike Nagi, Manatsu wears her heart on her sleeve.) The issue is that she has convinced herself that Manatsu is just "mistaking this pretend romance for real love", and that Manatsu deserves "someone much better".
The series implies that Nagi retroactively analyzes her affair with Manatsu as similar to the way her former tutor exploited her younger self's feelings. We of course know that's totally unfair, but Nagi's self-esteem may be so low that the idea that she doesn't deserve Manatsu came first, and the reasoning came after the fact. She might have felt a bit guilty about hiding her own motivations from Manatsu when they started their affair, and it's possible her mind used that as the seed of the excuse for why she doesn't deserve Manatsu.