How can your bag can get lost on nonstop flight ?

Simple... because every airport has at least one dumbass agent.

Our agent (Lets call him Donnie) happened to be working the gate yesterday. He boarded the flight but he was missing one person, who had checked in at the counter with one bag.

He paged this person twice, finally 10 mins prior to departure we decide to pull the bag and go.

We kept asking Donnie, did you check with the flight attendant to see how many people she has, maybe you forgot to pull the boarding pass.
Donnie, "Yes, I checked, I pulled all the boarding passes, he is not here."

English is Donnie's second language (barely)

I was working the ticket counter and ran up to the gate to check with the flight attendant, but it was too late, jet bridge was already pulled back.

Five minutes after the flight left I get a phone call.... (Donnie from the gate)... "Oh I just realized that I did not get a count from the flight attendant... and I found the boarding pass, it was just misplaced."

We send the bag on the next flight, arriving a few hours after the passenger.

That is one way a bag can get "lost" on a non-stop flight.... even if you checked in early.