<Raises hand>
Can I send my bags on an earlier flight and get $100?
Seriously, they do sometimes mis-count the number of pax boarded.
So the confusion about the number of empty seats does happen.
While I too would have been annoyed by the "fire drill" and separation from luggage, one of you could have gone on the earlier flight (with the bags).
I am assuming since you used the term companion that the other person is an adult. Obviously, if the other person is a child then you can't separate.
Good luck getting to BDL.