The selection of individual instances of a foliage HISM is broken, so that the instance is correctly outlined but the gizmo is placed over a different instance. If we delete the selected instance it will be the incorrect one under the gizmo.
In Foliage mode add a foliage asset and paint several instances into the level.
Select the foliage asset and then open the static mesh asset that it uses.
If it is not a nanite static mesh asset then set it to nanite and apply.
Back in the main window, in foliage mode, go to select mode and click on an instance of foliage.
Observe that the yellow selection highlight will be around the instance you clicked on, but in many cases the gizmo will be located on a different instance.
If you attempt to delete the selected instance it will NOT delete the highlighted instance but instead will delete the instance associated with where the gizmo is located.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-161498 in the post.