Thank you so much for taking the time to play and your valuable feedback!
Your initial instincts were actually correct - the idea is to have all targets lit up at the same time (and yes, the puzzle you posted is solvable in that way ;D). In the uploaded build it's a bug that allows a puzzle to be solved if a target was hit at least once at some point.
It has already been fixed, but we will upload the fix after the jam voting period has completed as it's not a game breaking bug (in fact, it's the opposite? =D)
If by 'ceiling puzzle' you are referring to the puzzle inside the ceiling of the shrine inside the village, then yes, that's a secret puzzle =)