Here's my personal little explanation for why Neptune wasn't at the Haven Academy fight. It's short, it's ridiculous, I hope you enjoy it.
"I'm coming, I'm coming, calm down." Neptune shouted as he ran towards the door. His words did nothing to stop the repeated knocking on his apartment door. He opened it, intending to yell at whoever was there, but when he saw who it was he instead pulled them into a tight hug.
Sun endured it for as long as he could before pushing away from Neptune. "Hey buddy, it's nice to see you too. Of course, it would have been much nicer to see you earlier this evening. You know, like we talked about!?" He barely managed to stop himself from screaming.
Neptune just seemed puzzled at his reply. "Yeah, well, that's hardly my fault. I was waiting there for you for hours. And, honestly, you should know me better than to let me sit alone in a coffee shop."
Sun gave him a slack-jawed stare. "Coffee shop? Why were you in a coffee shop? I told you to meet me on Haven grounds."
"Yes, exactly, Haven Grounds Coffee Shop. You know, just the place where we've met up countless times since we started at Haven. You didn't mean the school grounds, did you? It doesn't open until tomorrow, why would we have met there?"
"Because there was a massive White Fang attack? We were out there fighting a battle, we could have used some help!"
"Wait, what, the White Fang was here? They attacked the school? That's not at all what you said. You said you were fighting some massive hunger pangs, so we should meet up. Hence the coffee shop with the best late night food in town."
Sun was, at this point, barely stopping himself from ripping his hair out. Neptune wasn't much better, glaring at Sun in pure exasperation. "And when you heard the massive explosions nearby, you didn't think to check it out?"
"Of course I heard the fireworks. I would have gone to watch, too, but I don't abandon friends when they want to meet. Unlike some people I could mention."
Sun made a noise of pure frustration and started pacing back and forth, tail angrily lashing out. Neptune just stood with both hands on the doorframe, gripping it so tightly that it looked about ready to crack.
Suddenly, they both turned to each other and started laughing. They simultaneously went in for another hug, and Neptune pulled Sun into his apartment. "Okay, tell me exactly what happened."
"Well, it all started in Menagerie..."