Problem still exists in Unity 2018.2.1f1, it appears to also cause a nasty memory leak. Again when this happens if you click on one of the parent particle systems in the scene and then go under subemitters and click the linked gameobject in the field it will highlight the child emitters location in the scene hierarchy and you can see it will be under the wrong parent and not the expected parent. So somehow they are being jumbled and assigned the wrong parent, this only happens when they are instantiated through code. If you drag them in as prefabs they maintain their correct relationship.

I am seeing this issue on 2017.3.1.f1 Personal... It started happening today after I opened up my project. No changes had been made, so I can't give you any helpful steps to reproduce it. It doesn't seem to break anything though, just has an error message.

It it highlighting a regular scene object and the sub-emitters are clearly child objects of the system. Hope that helps.

I have this as well in 2018.1.6. Doesn't seem to affect anything. Just displaying a error message.

Update: even though these are being instaniated from a prefab, i have found that when many are spawned the children are actually being assigned to the wrong parent which is triggering the error. once they are all spawned while in play mode, if you look at one of the parent particle systems in the scene and then go under subemitters and click the linked gameobject in the field it will highlight the child emitters location in the scene hierarchy and you can see it will be under the wrong parent and not the expected parent.

I am having this seem issue in 2017.3.1p4, when spawned the sub emitters are correctly parented to the particle system that spawns them yet it produces this error. If I drag the prefab directly into the scene it doesnt produce the error but when it is instantiated it does.