Creepers are not dropping music discs in addition to their ordinary drops when killed by skeletons and the spigot release for 1.9.
I've tested with the vanilla server and spigot for both 1.8.8 and 1.9. Music discs drop as expected on all except spigot 1.9.
Steps to reproduce:
1. Spawn creeper
2. Spawn skeleton
3. Align self with creeper and skeleton so that skeleton arrows will hit creeper.
4. Enter survival mode if not and wait for skeleton to kill creeper.
A music disc is expected but not found.