I hate having to come right out and say it, but it's a fact. Dudes watch shows like RWBY specifically to waifu the mains. If you throw in a yuri pairing late in the game, it's essentially a signal to the audience that those characters are no longer waifu material, that they are forbidden to you. That's a recipe for a massive shitfit from the fans, no matter what, and it is easily avoided by making it clear from the outset that you intend to do same-sex pairings. For instance, nobody gets into watching Utena thinking that anyone in that show is going to be even remotely straight.I got into the fandom somewhere around early season 3. So yeah, it was around season 4 that the shipping quickly went from 'cute, occasionally weird but ultimately mostly harmless' to 'tumblr rainbow mafia shit'.
I, personally, don't watch shows to fixate on the protagonists to that degree, nor do I personally give a shit about shipping, much less shipping wars, but a lot of people do, and I can tell you from experience, you can't spring shit on people. As a writer, you have to telegraph your intentions to the audience well in advance, not throw shit in at the eleventh hour, after people have invested their precious time into multiple seasons of your show.