This is unfortunately a known issue with prespawned parented ghost prefabs. The fix from our side will take some foundational work that we have on our radar, but will take some time to do.
In the meantime as a workaround, there are two options.
1. In the GhostParent prefab, you can ensure that the nested GhostPrefab's are named the same. This is because we use the distinguish different prefabs of the same type, but since these prefabs are actually the same due to nested prefabs, there is some undefined behaviour going on.
2. Don't use multiple nested ghost prefabs in a parent prefab. You could parent them in the scene directly to organize them.