I just got back from a week trip (Banff is what they say it is =gorgeous).  My S.O. couldn't make it due to work obligations, so he bunny sat.  

I guess two nights ago (the evening before I came home), he woke up at like 1 or 2 am because Arduina and Leo had a fight.  He said there was lots of fur everywhere and he sprayed them both with water.  After that they have seemed fine.  They've been together for three weeks, and now just had a fight (first in well over a month).  Since they've been together, we've had no problems with them whatsoever, except for this one incident. 

I'm quite confused as to what happened and why and will it happen again??  

If they have no broken skin,and were fine afterwards, it was just a scuffle. They happen as rabbits get used to each other. Leave them together.

My Davey and Delilah are so bonded it is disgusting, and they get into little scuffles every once in a while, like what you described. Just part of living with another bunny. They will be fine.

Yeah, they've been fine. Just kinda weird, especially for 2am.

Maybe they were really missing me...