Dudeeee my heart!!.
Am I the only one doesnt think sempai had anything to do with their break up?.
Sempai is only one of several possibilities (that we know of), but she's the most obviously duplicitous and manipulative person that we've seen so far.
So if there is a reason for the breakup beyond Nene's loss of interest in/tolerance for Amane due to natural causes, sempai is the #1 suspect at this point, simply because she has a potential motive to separate the two.
Evidence against that theory: Nene seemed genuinely surprised that Hayama was aware that Nene and Amane had previously been in a romantic relationship. So if sempai did have anything to do with Nene's change in attitude, it would have had to have been indirectly.
Some other elements that haven't been mentioned: something that I myself have overstressed is Amane's surprise at the the graduation-day breakup; she specifically says that Nene had been getting distant all during their third year. BUT Nene still applied to the same high school.
That last part is one reason (of several) to see Nene's reason for the breakup as at least more ambiguous than her explanation--she had the opportunity to make a clean break then and didn't take it.