This is kinda how I feel about the Twin Theory in Kuroshitsuji/Black Butler. 
spoilers ahead
We didn’t really start seeing hints about it in the manga until after someone online started speculating about it. I don’t entirely remember how it started but I think (don’t quote me on this) is was because Ciel’s hairline kept shifting from one way to the other whenever we saw flashbacks of him with his father, Vincent. And then more hints were given out when it came to seeing him in the dungeon when he got kidnapped and made the contract with Sebastian. And then of course, we eventually find out he does have a twin! But that twin is the real Ciel Phantomhive, and the one we’re following has no name! (That may have changed though, I’ve not followed the manga in a while now)
While I do get it is nice to please your fans if it means staying relevant, but sometimes if you decide to confirm a theory after it was being made, then yeah, it was clearly an afterthought.