Who is messed up?

A World Without You - Beth Revis

I'm confused, Bo's confused and I can't read fast enough to ease my head.  Did Bo really take Sofia to the past and accidently leave her there or is all this a mind game?  Why did the "governmental officials" have to show up and mess with my comfortable read?  I was fine with their superpower abilities but no, they showed up and started shaking things up and now....its chaos!  I'm questioning everything I've read from the beginning, someone please start putting the answers together and quit adding more confusion.