It appears that only Bone Spear hits from the player are proccing Bone Prison (no thorough testing involved, just empirical evidence).
The wording on Bone Prison indicates that any instance of Bone Spear should be able to proc Bone Prison:
Bone Spear, Bone Spikes, and Bone Spirit have a 30% chance to trap enemies in a Bone Prison for 3 seconds.
Please fix simulacrum to allow the Bone Prison passive (30% chance to stun for 3s) to proc from simulacrum spears.
If this isn’t considered a bug, then please increase the % chance on bone prison to compensate, and update the Bone Prison passive description to indicate that this only affects spells cast from the player.