There’s so many things! First off, where’s Mulder’s DNA test? But most of all, I refuse that this is the way they finally find their son after 17 years. That is waaaaaay too easy. They just happen to be on a case, and bam! William! And he’s dead. Then he isn’t anymore. Then it’s maybe not him. But then he’s a total jerk with two girlfriends and he gets off making kill each other. 
This is the X-Files and I trust no one, especially not when things seem too easy and simple to be real.