The fluke? I assume you are referring to what Willow refers to as the “clothes fluke” after she shares a kiss with Xander? I bet there’s a ton of different interpretations for this, but what I always gathered was that they were best friends and it sort of begged the question if they could have been anything more. You see this in Becoming Part 2 when Xander sees Willow lying on the hospital bed and he confesses to her that she’s his best friend and he loves her. But although she immediately wakes on his confession, she is calling out Oz’s name in a daze, and Oz immediately walks in. But there is a look of disappointment that crosses Xander’s face: right as he tells her he loves her, she calls out Oz’s name instead. And that disappoints him, and I think it’s because he always took Willow for granted, how she was always there for him, sort of always “his” in a way. Now he’s starting to realize that Willow does not just belong to him, that she is dating someone else, that she can fall in love with someone else and he’s suddenly afraid of losing her. In the hospital speech, he even says they talk on the phone everyday and tell each other how their day went. He’s worried about losing that, losing her. And Willow has always had feelings for Xander and so when they see each other all dressed up, it sort of lets them see their grown up selves. I think Xander always sort of knew after high school he was never going to be in any sort of long-term relationship with Cordelia, and he was probably wondering if Willow was right for him after all. And Willow, who always had feelings for Xander, always probably sort of wondered if things would lead her right back to Xander in the end and if they would ultimately end up together, which led to them kissing. But as soon as they did it they realized it was “too soon” because although they were both thinking about the future, both of them were in committed relationships that they didn’t want to screw up, Willow most of all. To sum it all up, it was basically a case of “we’re friends now but what if we are always meant to be together and we’re missing out?” I don’t know, I start recapping season 3 pretty soon so I am eager to see that scene again, but ultimately I think it was also to serve the plot so that Cordelia would leave Sunnydale and head over to LA with Angel. And Willow’s relationship with Oz was always sort of idyllic and peaceful, so of course there needs to be some sort of drama thrown in, because no one’s ever truly happy in Sunnydale! :P I hope this answers your question!
Oh, and last thought, I swear: This had to really have happened now, in season 3, instead of any other time during the show because in season 4, Willow starts experimenting with her sexuality and starts her relationship with Tara so it would be weird for her to say, “I like girls now” and then start having confused feelings over Xander. At least in my opinion! And Xander starts his relationship with Anya that continues into his doomed-relationship arc, so yeah, there wasn’t really a better time to explore that, but considering how much Willow pined after Xander in season 1, it had to come up at some point!
