Yep...happened to me too on both the iPhone and iPad (both running IOS 10). Occurred after I updated to IOS 10.0.2. Only playlist affected were "smart playlist". Specifically, a number of smart playlist I created showed up on both devices with no entries even though songs appear correctly listed via iTunes on my computer.
My (PITA) workaround was to review all playlist on both devices, delete any problem smart playlist on my computer, sync both devices, then recreate the smart playlist on the computer, select same playlist on each device, then sync again. Once done all playlist now correctly show their contents.