If I found an iPhone on top of a paper boarding pass and decided to pick it up to turn it in to lost and found, I'd probably pick up both, since the name/PNR on the boarding pass would help reunite the phone with its owner. If I had time, I'd even go to the gate for that flight and give it to the GA so they could page the passenger at the gate.
Seems it could have been:
(1) someone thought it was unattended, picked it up to turn it in (and failed to grab the boarding pass)
(2) someone picked it up thinking it was theirs, later realized they had two phones, turned it in
(3) someone stole it from the bathroom, later decided it wasn't worth it and dropped it off somewhere where it was later found and turned in (or maybe even turned it in themselves)
(4) OP actually set it down somewhere other than where they thought they did (a different sink, on the hand dryer, fell out of their purse in the terminal, etc.) and it was found there.
I think we will never know for sure!